Hi Edward,
Thank you again for your reply.
Here are some clarifications:
1. I have attached the script I am using (full_analysis-sphere.py).
2. In fact, SEQ_ARGS[6] is set to an integer value of 2, which refers to
the spin_name_col in my .seq file:
................
14 GLY N
15 ALA N
16 GLN N
.................
That part works well for me now. However, if I don't set the
spin_name_col, and rely on the code you added (... spin.name(HET_NAME)),
I get the following error:
relax> spin.name(spin_id='N', name=None)
RelaxError: The new spin name argument None must be a string.
3. The problem is:
If I use this script (with the -d option) with the "spin_id='@N'" (like
I said in the previous message), I don't have warnings in the log, see
the "log-with-spin_id" file
But if I don't put "spin_id='@N'", I have several Warnings (which do not
stop relax), see the "log-without-spin_id" file. The warnings are just
before the "The main class" part in the log.
I don't see these warnings without the -d option. Maybe it is not a
problem, but I am not sure...
Cheers,
PY
Edward d'Auvergne wrote:
Hi,
Would you be able to attach the script you are using? Setting
SEQ_ARGS[6] to the string value of 'N' should not be possible, it
needs to be an integer. Could you also post a single line from the
file you are reading the protein sequence from? Oh, it would also be
useful if you attach a log of the relax print outs (this might be
obvious, but "$ relax full_analysis.py > log" will generate the 'log'
file which can be attached).
Cheers,
Edward
On Tue, Feb 10, 2009 at 10:17 PM, Pierre-Yves Savard
<Pierre-Yves.Savard@xxxxxxxxxxxxx> wrote:
Hello,
It seems to work if I both define the name of the spin to 'N' with the
SEQ_ARGS[6] argument (that is including the spin name, here 'N', in the
sequence file) AND add the argument "spin_id='@N'" in the function
strcutre.vector(), part of the section "Diffusion models MII to MV" (see
last line of the following pasted text):
# Diffusion models MII to MV.
#############################
elif DIFF_MODEL == 'sphere' or DIFF_MODEL == 'prolate' or
DIFF_MODEL == 'oblate' or DIFF_MODEL == 'ellipsoid':
# Loop until convergence if CONV_LOOP is set, otherwise just
loop once.
# This looping could be made much cleaner by removing the
dependence on the determine_rnd() function.
while 1:
# Determine which round of optimisation to do (init,
round_1, round_2, etc).
self.round = self.determine_rnd(model=DIFF_MODEL)
# Inital round of optimisation for diffusion models MII
to MV.
if self.round == 0:
# Base directory to place files into.
self.base_dir = DIFF_MODEL + '/init/'
# Run name.
name = DIFF_MODEL
# Create the data pipe.
pipe.create(name, 'mf')
# Load the local tm diffusion model MI results.
results.read(file='results', dir='local_tm/aic')
# Remove the tm parameter.
model_free.remove_tm()
# Deselect the spins in the EXCLUDE list.
if EXCLUDE:
deselect.read(file=EXCLUDE)
# Load the PDB file and calculate the unit vectors
parallel to the XH bond.
if PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H', spin_id='@N')
However, if the SEQ_ARGS[6] argument is set to None, and, thus, the
following code (you added today) takes care of the spin name:
# Name the spins if necessary.
if SEQ_ARGS[6] == None:
spin.name(HET_NAME)
the following error message is thrown:
Traceback (most recent call last):
File "./full_analysis-prolate.py", line 641, in <module>
Main(self.relax)
File "./full_analysis-prolate.py", line 264, in __init__
self.multi_model()
File "./full_analysis-prolate.py", line 600, in multi_model
spin.name(HET_NAME)
File "/usr/local/packages/relax-1.3/prompt/spin.py", line 269, in name
raise RelaxStrError, ('new spin name', name)
RelaxStrError: RelaxError: The new spin name argument None must be a
string.
Do you have any clue of what is happening ?
Thanks
Pierre-Yves
Pierre-Yves Savard wrote:
Hi Edward,
Thank you for your quick answer.
I tried with the new script, defining the name of the spin to N with the
SEQ_ARGS[6] argument, but I still encounter the following error messages
(which I also get when SEQ_ARGS[6]=None):
relax> structure.vectors(attached='H', spin_id=None, model=None,
verbosity=1, ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
Traceback (most recent call last):
File "/usr/local/packages/relax-1.3/relax", line 418, in <module>
Relax()
File "/usr/local/packages/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/usr/local/packages/relax-1.3/prompt/interpreter.py", line 273,
in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/usr/local/packages/relax-1.3/prompt/interpreter.py", line 534,
in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/usr/local/packages/relax-1.3/prompt/interpreter.py", line 430,
in interact_script
execfile(script_file, local)
File "full_analysis-sphere.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere.py", line 230, in __init__
structure.vectors(attached='H')
File "/usr/local/packages/relax-1.3/prompt/structure.py", line 586, in
vectors
generic_fns.structure.main.vectors(attached=attached,
spin_id=spin_id, model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/usr/local/packages/relax-1.3/generic_fns/structure/main.py",
line 353, in vectors
warn(RelaxWarning("Either the spin number or name must be set for
the spin " + `id` + " to identify the corresponding atom in the
molecule."))
RelaxWarning: Either the spin number or name must be set for the spin
':15' to identify the corresponding atom in the molecule.
I checked the pdb and names are fine:
...
ATOM 31 N ASN 6 -21.732 2.728 -13.120 1.00 25.52
ATOM 32 H ASN 6 -11.923 7.967 -12.183 1.00 0.00
...
Thank you,
Pierre-Yves
Edward d'Auvergne wrote:
Hi,
The addition of spin_id='@N' should not be necessary if the sequence
data you have loaded using this script has the atom/spin name set to
'N'. If not, I have modified the full_analysis.py script in the
repository 1.3 line to name your spins in that way. The problem is
that the spins are unnamed so they cannot be matched to anything in
the PDB file. Hence the NH bond vectors are not extracted for any
spins. Then when it comes to optimisation, all the spins without bond
vector information are deselected. But as this is all spins, then
there are essentially no model-free models to optimise and there is
only the diffusion tensor. But this is fixed by the fix() function,
the one you can't fix and can't be fixed. So as the only parameters
remaining are those of the diffusion tensor, and these are fixed,
relax cannot do anything. There should be warning messages describing
this problem much further up in the script. I would guess thought
that they have been suppressed by your addition in point one, as there
are no spins with a spin id of '@N' and hence no NH bond vectors will
be loaded.
Regards,
Edward
On Tue, Feb 10, 2009 at 5:00 PM, Pierre-Yves Savard
<Pierre-Yves.Savard@xxxxxxxxxxxxx> wrote:
Hi,
I am starting a new relax analysis with the full_analysis.py script,
together with relax 1.3 revision 8769. I performed the first step,
'local_tm', with success.
However, for what concerns diffusion models 'sphere', 'prolate', 'oblate
and 'ellipsoid', I encountered the following errors:
1. I had to add: "spin_id='@N'" in the function structure.vector()
in order to read the pdb and extract vectors properly:
# Load the PDB file and calculate the unit vectors parallel to
the XH bond.
if not local_tm and PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H', spin_id='@N')
...
# Load the PDB file and calculate the unit vectors parallel to
the XH bond.
if PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H', spin_id='@N')
2. Then, I encountered the following error message (using the debug
option -d) when trying to optimise models 'prolate', 'oblate' and
'ellipsoid':
Traceback (most recent call last):
File "full_analysis_prolate.py", line 640, in <module>
Main(self.relax)
File "full_analysis_prolate.py", line 267, in __init__
self.multi_model()
File "full_analysis_prolate.py", line 631, in multi_model
grid_search(inc=GRID_INC)
File "/usr/local/packages/relax-1.3/prompt/minimisation.py", line 156,
in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/usr/local/packages/relax-1.3/generic_fns/minimise.py", line
185, in grid_search
grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File
"/usr/local/packages/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 479, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File
"/usr/local/packages/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 788, in minimise
model_type = self.determine_model_type()
File "/usr/local/packages/relax-1.3/specific_fns/model_free/main.py",
line 1026, in determine_model_type
raise RelaxError, "All parameters are fixed."
RelaxError: RelaxError: All parameters are fixed.
There seems to be a problem with the fix() function, although I was not
able to fix (!) it...
Thank you very much for your help,
Pierre-Yves
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[?1034h
relax repository checkout
Protein dynamics by NMR relaxation data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2009 the relax development team
This is free software which you are welcome to modify and redistribute under
the conditions of the
GNU General Public License (GPL). This program, including all modules, is
licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL'. Assistance
in using this program
can be accessed by typing 'help'.
script = 'full_analysis-sphere-error.py'
----------------------------------------------------------------------------------------------------
##############################################################################
#
#
# Copyright (C) 2004-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
# relax is free software; you can redistribute it and/or modify
#
# it under the terms of the GNU General Public License as published by
#
# the Free Software Foundation; either version 2 of the License, or
#
# (at your option) any later version.
#
#
#
# relax is distributed in the hope that it will be useful,
#
# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
# GNU General Public License for more details.
#
#
#
# You should have received a copy of the GNU General Public License
#
# along with relax; if not, write to the Free Software
#
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
#
###############################################################################
"""Script for black-box model-free analysis.
This script is designed for those who appreciate black-boxes or those who
appreciate complex code. Importantly data at multiple magnetic field
strengths is essential for this analysis. The script will need to be heavily
tailored to the molecule in question by changing the variables just below
this documentation. If you would like to change how model-free analysis is
performed, the code in the class Main can be changed as needed. For a
description of object-oriented coding in python using classes,
functions/methods, self, etc., see the python tutorial.
How to use this script
======================
The value of the variable DIFF_MODEL will determine the behaviour of this
script. The five diffusion models used in this script are:
Model I (MI) - Local tm.
Model II (MII) - Sphere.
Model III (MIII) - Prolate spheroid.
Model IV (MIV) - Oblate spheroid.
Model V (MV) - Ellipsoid.
Model I must be optimised prior to any of the other diffusion models, while
the Models II to V can be optimised in any order. To select the various
models, set the variable DIFF_MODEL to the following strings:
MI - 'local_tm'
MII - 'sphere'
MIII - 'prolate'
MIV - 'oblate'
MV - 'ellipsoid'
This approach has the advantage of eliminating the need for an initial
estimate of a global diffusion tensor and removing all the problems
associated with the initial estimate.
It is important that the number of parameters in a model does not exceed the
number of relaxation data sets for that spin. If this is the case, the list
of models in the MF_MODELS and LOCAL_TM_MODELS variables will need to be
trimmed.
Model I - Local tm
~~~~~~~~~~~~~~~~~~
This will optimise the diffusion model whereby all spin of the molecule have
a local tm value, i.e. there is no global diffusion tensor. This model needs
to be optimised prior to optimising any of the other diffusion models. Each
spin is fitted to the multiple model-free models separately, where the
parameter tm is included in each model.
AIC model selection is used to select the models for each spin.
Model II - Sphere
~~~~~~~~~~~~~~~~~
This will optimise the isotropic diffusion model. Multiple steps are
required, an initial optimisation of the diffusion tensor, followed by a
repetitive optimisation until convergence of the diffusion tensor. Each of
these steps requires this script to be rerun. For the initial optimisation,
which will be placed in the directory './sphere/init/', the following steps
are used:
The model-free models and parameter values for each spin are set to those of
diffusion model MI.
The local tm parameter is removed from the models.
The model-free parameters are fixed and a global spherical diffusion tensor
is minimised.
For the repetitive optimisation, each minimisation is named from 'round_1'
onwards. The initial 'round_1' optimisation will extract the diffusion
tensor from the results file in './sphere/init/', and the results will be
placed in the directory './sphere/round_1/'. Each successive round will take
the diffusion tensor from the previous round. The following steps are used:
The global diffusion tensor is fixed and the multiple model-free models are
fitted to each spin.
AIC model selection is used to select the models for each spin.
All model-free and diffusion parameters are allowed to vary and a global
optimisation of all parameters is carried out.
Model III - Prolate spheroid
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that
an axially symmetric diffusion tensor with Da >= 0 is used. The base
directory containing all the results is './prolate/'.
Model IV - Oblate spheroid
~~~~~~~~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that
an axially symmetric diffusion tensor with Da <= 0 is used. The base
directory containing all the results is './oblate/'.
Model V - Ellipsoid
~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that a
fully anisotropic diffusion tensor is used (also known as rhombic or
asymmetric diffusion). The base directory is './ellipsoid/'.
Final run
~~~~~~~~~
Once all the diffusion models have converged, the final run can be executed.
This is done by setting the variable DIFF_MODEL to 'final'. This consists of
two steps, diffusion tensor model selection, and Monte Carlo simulations.
Firstly AIC model selection is used to select between the diffusion tensor
models. Monte Carlo simulations are then run solely on this selected
diffusion model. Minimisation of the model is bypassed as it is assumed that
the model is already fully optimised (if this is not the case the final run
is not yet appropriate).
The final black-box model-free results will be placed in the file
'final/results'.
"""
# Python module imports.
from os import getcwd, listdir
from re import search
from string import lower
# relax module imports.
from float import floatAsByteArray
from generic_fns.mol_res_spin import generate_spin_id, spin_index_loop,
spin_loop
from generic_fns import pipes
from relax_errors import RelaxError
# User variables.
#################
# The diffusion model.
DIFF_MODEL = 'sphere'
# The model-free models (do not change these unless absolutely necessary).
MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9']
# The PDB file (set this to None if no structure is available).
PDB_FILE = 'PROT-b-relax.pdb'
# The sequence data (file name, dir, mol_name_col, res_num_col, res_name_col,
spin_num_col, spin_name_col, sep). These are the arguments to the
sequence.read() user function, for more information please see the
documentation for that function.
SEQ_ARGS = ['1S56b_with_name.seq', None, None, 0, 1, None, 2, None]
# The heteronucleus atom name corresponding to that of the PDB file (used if
the spin name is not in the sequence data).
HET_NAME = 'N'
# The relaxation data (data type, frequency label, frequency, file name, dir,
mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, sep).
These are the arguments to the relax_data.read() user function, please see
the documentation for that function for more information.
RELAX_DATA = [['R1', '800', 799.737 * 1e6, 'R1-800', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '800', 799.737 * 1e6, 'R2-800', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '800', 799.737 * 1e6, 'noe-800', None, None, 0, 1,
None, None, 2, 3, None],
['R1', '600', 599.737 * 1e6, 'R1-600', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '600', 599.737 * 1e6, 'R2-600', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '600', 599.737 * 1e6, 'noe-600', None, None, 0, 1,
None, None, 2, 3, None],
['R1', '500', 499.719 * 1e6, 'R1-500', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '500', 499.719 * 1e6, 'R2-500', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '500', 499.719 * 1e6, 'noe-500', None, None, 0, 1,
None, None, 2, 3, None]
]
# The file containing the list of unresolved spins to exclude from the
analysis (set this to None if no spin is to be excluded).
UNRES = 'prolines'
# A file containing a list of spins which can be dynamically excluded at any
point within the analysis (when set to None, this variable is not used).
EXCLUDE = 'prolines'
# The bond length, CSA values, heteronucleus type, and proton type.
BOND_LENGTH = 1.02 * 1e-10
CSA = -172 * 1e-6
HETNUC = '15N'
PROTON = '1H'
# The grid search size (the number of increments per dimension).
GRID_INC = 11
# The optimisation technique.
MIN_ALGOR = 'newton'
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
MC_NUM = 500
# Automatic looping over all rounds until convergence (must be a boolean
value of True or False).
CONV_LOOP = True
class Main:
def __init__(self, relax):
"""Execute the model-free analysis."""
# Setup.
self.relax = relax
# MI - Local tm.
################
if DIFF_MODEL == 'local_tm':
# Base directory to place files into.
self.base_dir = 'local_tm/'
# Sequential optimisation of all model-free models (function must
be modified to suit).
self.multi_model(local_tm=True)
# Model selection.
self.model_selection(modsel_pipe='aic', dir=self.base_dir + 'aic')
# Diffusion models MII to MV.
#############################
elif DIFF_MODEL == 'sphere' or DIFF_MODEL == 'prolate' or DIFF_MODEL
== 'oblate' or DIFF_MODEL == 'ellipsoid':
# Loop until convergence if CONV_LOOP is set, otherwise just loop
once.
# This looping could be made much cleaner by removing the
dependence on the determine_rnd() function.
while 1:
# Determine which round of optimisation to do (init, round_1,
round_2, etc).
self.round = self.determine_rnd(model=DIFF_MODEL)
# Inital round of optimisation for diffusion models MII to MV.
if self.round == 0:
# Base directory to place files into.
self.base_dir = DIFF_MODEL + '/init/'
# Run name.
name = DIFF_MODEL
# Create the data pipe.
pipe.create(name, 'mf')
# Load the local tm diffusion model MI results.
results.read(file='results', dir='local_tm/aic')
# Remove the tm parameter.
model_free.remove_tm()
# Deselect the spins in the EXCLUDE list.
if EXCLUDE:
deselect.read(file=EXCLUDE)
# Load the PDB file and calculate the unit vectors
parallel to the XH bond.
if PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H', spin_id='@N')
# Add an arbitrary diffusion tensor which will be
optimised.
if DIFF_MODEL == 'sphere':
diffusion_tensor.init(10e-9, fixed=False)
inc = 11
elif DIFF_MODEL == 'prolate':
diffusion_tensor.init((10e-9, 0, 0, 0),
spheroid_type='prolate', fixed=False)
inc = 11
elif DIFF_MODEL == 'oblate':
diffusion_tensor.init((10e-9, 0, 0, 0),
spheroid_type='oblate', fixed=False)
inc = 11
elif DIFF_MODEL == 'ellipsoid':
diffusion_tensor.init((10e-09, 0, 0, 0, 0, 0),
fixed=False)
inc = 6
# Minimise just the diffusion tensor.
fix('all_spins')
grid_search(inc=inc)
minimise(MIN_ALGOR)
# Write the results.
results.write(file='results', dir=self.base_dir,
force=True)
# Normal round of optimisation for diffusion models MII to MV.
else:
# Base directory to place files into.
self.base_dir = DIFF_MODEL + '/round_' + `self.round` +
'/'
# Load the optimised diffusion tensor from either the
previous round.
self.load_tensor()
# Sequential optimisation of all model-free models
(function must be modified to suit).
self.multi_model()
# Model selection.
self.model_selection(modsel_pipe='final',
dir=self.base_dir + 'aic')
# Final optimisation of all diffusion and model-free
parameters.
fix('all', fixed=False)
# Minimise all parameters.
minimise(MIN_ALGOR)
# Write the results.
dir = self.base_dir + 'opt'
results.write(file='results', dir=dir, force=True)
# Test for convergence.
converged = self.convergence()
# Break out of the infinite while loop if automatic
looping is not activated or if convergence has occurred.
if converged or not CONV_LOOP:
break
# Final run.
############
elif DIFF_MODEL == 'final':
# Diffusion model selection.
############################
# All the global diffusion models to be used in the model
selection.
self.pipes = ['local_tm', 'sphere', 'prolate', 'oblate',
'ellipsoid']
# Create the local_tm data pipe.
pipe.create('local_tm', 'mf')
# Load the local tm diffusion model MI results.
results.read(file='results', dir='local_tm/aic')
# Loop over models MII to MV.
for model in ['sphere', 'prolate', 'oblate', 'ellipsoid']:
# Determine which was the last round of optimisation for each
of the models.
self.round = self.determine_rnd(model=model) - 1
# If no directories begining with 'round_' exist, the script
has not been properly utilised!
if self.round < 1:
# Construct the name of the diffusion tensor.
name = model
if model == 'prolate' or model == 'oblate':
name = name + ' spheroid'
# Throw an error to prevent misuse of the script.
raise RelaxError, "Multiple rounds of optimisation of the
" + name + " (between 8 to 15) are required for the proper execution of this
script."
# Create the data pipe.
pipe.create(model, 'mf')
# Load the diffusion model results.
results.read(file='results', dir=model + '/round_' +
`self.round` + '/opt')
# Model selection between MI to MV.
self.model_selection(modsel_pipe='final', write_flag=False)
# Monte Carlo simulations.
##########################
# Fix the diffusion tensor, if it exists.
if hasattr(pipes.get_pipe('final'), 'diff_tensor'):
fix('diff')
# Simulations.
monte_carlo.setup(number=MC_NUM)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise(MIN_ALGOR)
eliminate()
monte_carlo.error_analysis()
# Write the final results.
##########################
results.write(file='results', dir='final', force=True)
# Unknown script behaviour.
###########################
else:
raise RelaxError, "Unknown diffusion model, change the value of
'DIFF_MODEL'"
def convergence(self):
"""Test for the convergence of the global model."""
# Alias the data pipes.
cdp = pipes.get_pipe()
prev_pipe = pipes.get_pipe('previous')
# Print out.
print "\n\n\n"
print "#####################"
print "# Convergence tests #"
print "#####################\n\n"
# Convergence flags.
chi2_converged = True
models_converged = True
params_converged = True
# Chi-squared test.
###################
print "Chi-squared test:"
print " chi2 (k-1): " + `prev_pipe.chi2`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_pipe.chi2)` + ')'
print " chi2 (k): " + `cdp.chi2`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(cdp.chi2)` + ')'
print " chi2 (difference): " + `prev_pipe.chi2 - cdp.chi2`
if prev_pipe.chi2 == cdp.chi2:
print " The chi-squared value has converged.\n"
else:
print " The chi-squared value has not converged.\n"
chi2_converged = False
# Identical model-free model test.
##################################
print "Identical model-free models test:"
# Create a string representation of the model-free models of the
previous data pipe.
prev_models = ''
for spin in spin_loop(pipe='previous'):
if hasattr(spin, 'model'):
if not spin.model == 'None':
prev_models = prev_models + spin.model
# Create a string representation of the model-free models of the
current data pipe.
curr_models = ''
for spin in spin_loop():
if hasattr(spin, 'model'):
if not spin.model == 'None':
curr_models = curr_models + spin.model
# The test.
if prev_models == curr_models:
print " The model-free models have converged.\n"
else:
print " The model-free models have not converged.\n"
models_converged = False
# Identical parameter value test.
#################################
print "Identical parameter test:"
# Only run the tests if the model-free models have converged.
if models_converged:
# Diffusion parameter array.
if DIFF_MODEL == 'sphere':
params = ['tm']
elif DIFF_MODEL == 'oblate' or DIFF_MODEL == 'prolate':
params = ['tm', 'Da', 'theta', 'phi']
elif DIFF_MODEL == 'ellipsoid':
params = ['tm', 'Da', 'Dr', 'alpha', 'beta', 'gamma']
# Tests.
for param in params:
# Get the parameter values.
prev_val = getattr(prev_pipe.diff_tensor, param)
curr_val = getattr(cdp.diff_tensor, param)
# Test if not identical.
if prev_val != curr_val:
print " Parameter: " + param
print " Value (k-1): " + `prev_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " Value (k): " + `curr_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(curr_val)` + ')'
print " The diffusion parameters have not converged.\n"
params_converged = False
# Skip the rest if the diffusion tensor parameters have not
converged.
if params_converged:
# Loop over the spins.
for mol_index, res_index, spin_index in spin_index_loop():
# Alias the spin containers.
prev_spin =
prev_pipe.mol[mol_index].res[res_index].spin[spin_index]
curr_spin =
cdp.mol[mol_index].res[res_index].spin[spin_index]
# Skip if the parameters have not converged.
if not params_converged:
break
# Skip spin systems with no 'params' object.
if not hasattr(prev_spin, 'params') or not
hasattr(curr_spin, 'params'):
continue
# The spin ID string.
spin_id =
generate_spin_id(mol_name=cdp.mol[mol_index].name,
res_num=cdp.mol[mol_index].res[res_index].num,
res_name=cdp.mol[mol_index].res[res_index].name,
spin_num=cdp.mol[mol_index].res[res_index].spin[spin_index].num,
spin_name=cdp.mol[mol_index].res[res_index].spin[spin_index].name)
# Loop over the parameters.
for j in xrange(len(curr_spin.params)):
# Get the parameter values.
prev_val = getattr(prev_spin,
lower(prev_spin.params[j]))
curr_val = getattr(curr_spin,
lower(curr_spin.params[j]))
# Test if not identical.
if prev_val != curr_val:
print " Spin ID: " + `spin_id`
print " Parameter: " + curr_spin.params[j]
print " Value (k-1): " + `prev_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " Value (k): " + `curr_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " The model-free parameters have not
converged.\n"
params_converged = False
break
# The model-free models haven't converged hence the parameter values
haven't converged.
else:
print " The model-free models haven't converged hence the
parameters haven't converged.\n"
params_converged = False
# Print out.
if params_converged:
print " The diffusion tensor and model-free parameters have
converged.\n"
# Final print out.
##################
print "\nConvergence:"
if chi2_converged and models_converged and params_converged:
print " [ Yes ]"
return True
else:
print " [ No ]"
return False
def determine_rnd(self, model=None):
"""Function for returning the name of next round of optimisation."""
# Get a list of all files in the directory model. If no directory
exists, set the round to 'init' or 0.
try:
dir_list = listdir(getcwd() + '/' + model)
except:
return 0
# Set the round to 'init' or 0 if there is no directory called 'init'.
if 'init' not in dir_list:
return 0
# Create a list of all files which begin with 'round_'.
rnd_dirs = []
for file in dir_list:
if search('^round_', file):
rnd_dirs.append(file)
# Create a sorted list of integer round numbers.
numbers = []
for dir in rnd_dirs:
try:
numbers.append(int(dir[6:]))
except:
pass
numbers.sort()
# No directories begining with 'round_' exist, set the round to 1.
if not len(numbers):
return 1
# Determine the number for the next round (add 1 to the highest
number).
return numbers[-1] + 1
def load_tensor(self):
"""Function for loading the optimised diffusion tensor."""
# Create the data pipe for the previous data (deleting the old data
pipe first if necessary).
if pipes.has_pipe('previous'):
pipe.delete('previous')
pipe.create('previous', 'mf')
# Load the optimised diffusion tensor from the initial round.
if self.round == 1:
results.read('results', DIFF_MODEL + '/init')
# Load the optimised diffusion tensor from the previous round.
else:
results.read('results', DIFF_MODEL + '/round_' + `self.round - 1`
+ '/opt')
def model_selection(self, modsel_pipe=None, dir=None, write_flag=True):
"""Model selection function."""
# Model elimination.
if modsel_pipe != 'final':
eliminate()
# Model selection (delete the model selection pipe if it already
exists).
if pipes.has_pipe(modsel_pipe):
pipe.delete(modsel_pipe)
model_selection(method='AIC', modsel_pipe=modsel_pipe,
pipes=self.pipes)
# Write the results.
if write_flag:
results.write(file='results', dir=dir, force=True)
def multi_model(self, local_tm=False):
"""Function for optimisation of all model-free models."""
# Set the data pipe names (also the names of preset model-free
models).
if local_tm:
self.pipes = LOCAL_TM_MODELS
else:
self.pipes = MF_MODELS
# Loop over the data pipes.
for name in self.pipes:
# Create the data pipe.
if pipes.has_pipe(name):
pipe.delete(name)
pipe.create(name, 'mf')
# Load the sequence.
sequence.read(SEQ_ARGS[0], SEQ_ARGS[1], SEQ_ARGS[2], SEQ_ARGS[3],
SEQ_ARGS[4], SEQ_ARGS[5], SEQ_ARGS[6], SEQ_ARGS[7])
# Name the spins if necessary.
if SEQ_ARGS[6] == None:
spin.name(HET_NAME)
# Load the PDB file and calculate the unit vectors parallel to
the XH bond.
if not local_tm and PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H')
# Load the relaxation data.
for data in RELAX_DATA:
relax_data.read(data[0], data[1], data[2], data[3], data[4],
data[5], data[6], data[7], data[8], data[9], data[10], data[11], data[12])
# Deselect spins to be excluded (including unresolved and
specifically excluded spins).
if UNRES:
deselect.read(file=UNRES)
if EXCLUDE:
deselect.read(file=EXCLUDE)
# Copy the diffusion tensor from the 'opt' data pipe and prevent
it from being minimised.
if not local_tm:
diffusion_tensor.copy('previous')
fix('diff')
# Set all the necessary values.
value.set(BOND_LENGTH, 'bond_length')
value.set(CSA, 'csa')
value.set(HETNUC, 'heteronucleus')
value.set(PROTON, 'proton')
# Select the model-free model.
model_free.select_model(model=name)
# Minimise.
grid_search(inc=GRID_INC)
minimise(MIN_ALGOR)
# Write the results.
dir = self.base_dir + name
results.write(file='results', dir=dir, force=True)
# The main class.
Main(self.relax)
----------------------------------------------------------------------------------------------------
relax> pipe.create(pipe_name='sphere', pipe_type='mf')
relax> results.read(file='results', dir='local_tm/aic')
Opening the file 'local_tm/aic/results.bz2' for reading.
relax> model_free.remove_tm(spin_id=None)
relax> deselect.read(file='prolines', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, change_all=False)
Opening the file 'prolines' for reading.
relax> structure.read_pdb(file='PROT-b-relax.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file 'PROT-b-relax.pdb' for reading.
Adding molecule 'PROT-b-relax_mol1' to model None (from the original molecule
number 1 of model None)
relax> structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1,
ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=False)
relax> fix(element='all_spins', fixed=True)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
Only diffusion tensor parameters will be used.
Unconstrained grid search size: 11 (constraints may decrease this size).
Grid search
~~~~~~~~~~~
Searching the grid.
k: 0 xk: array([ 1000.])
fk: 1954444.19194
k: 1 xk: array([ 2100.])
fk: 1820500.71446
k: 2 xk: array([ 3200.])
fk: 1566147.00045
k: 3 xk: array([ 4300.])
fk: 1113645.19427
k: 4 xk: array([ 5400.])
fk: 718986.774228
k: 5 xk: array([ 6500.])
fk: 431715.565165
k: 6 xk: array([ 7600.])
fk: 237782.247308
k: 7 xk: array([ 8700.])
fk: 116130.130301
k: 8 xk: array([ 9800.])
fk: 50701.3406668
k: 9 xk: array([ 10900.])
fk: 30873.1176452
Parameter values: array([ 10900.])
Function value: 30873.1176452
Iterations: 11
Function calls: 11
Gradient calls: 0
Hessian calls: 0
Warning: None
relax> minimise(*args=('newton',), func_tol=1e-25, max_iterations=10000000,
constraints=True, scaling=True, verbosity=1)
Only diffusion tensor parameters will be used.
Method of Multipliers
~~~~~~~~~~~~~~~~~~~~~
k: 0 xk: array([ 10900.])
fk: 30873.1176452
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 10900.])
fk: 30873.1176452
Parameter values: array([ 10886.25622282])
Function value: 30870.1005268
Iterations: 1
Function calls: 3
Gradient calls: 2
Hessian calls: 1
Warning: None
k: 1 xk: array([ 10886.25622282])
fk: 30870.1005268
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 10886.25622282])
fk: 30870.1005268
Parameter values: array([ 10886.26769994])
Function value: 30870.1005246
Iterations: 1
Function calls: 3
Gradient calls: 2
Hessian calls: 1
Warning: None
k: 2 xk: array([ 10886.26769994])
fk: 30870.1005246
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 10886.26769994])
fk: 30870.1005246
Parameter values: array([ 10886.26769994])
Function value: 30870.1005246
Iterations: 1
Function calls: 5
Gradient calls: 2
Hessian calls: 1
Warning: None
k: 3 xk: array([ 10886.26769994])
fk: 30870.1005246
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 10886.26769994])
fk: 30870.1005246
Parameter values: array([ 10886.26769994])
Function value: 30870.1005246
Iterations: 1
Function calls: 16
Gradient calls: 2
Hessian calls: 1
Warning: None
Parameter values: array([ 10886.26769994])
Function value: 30870.1005246
Iterations: 4
Function calls: 27
Gradient calls: 8
Hessian calls: 4
Warning: None
relax> results.write(file='results', dir='sphere/init/', force=True,
compress_type=1)
Opening the file 'sphere/init//results.bz2' for writing.
relax> pipe.create(pipe_name='previous', pipe_type='mf')
relax> results.read(file='results', dir='sphere/init')
Opening the file 'sphere/init/results.bz2' for reading.
relax> pipe.create(pipe_name='m0', pipe_type='mf')
relax> sequence.read(file='1S56b_with_name.seq', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=2, sep=None)
Opening the file '1S56b_with_name.seq' for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 2 GLY None N
None 3 LEU None N
None 4 LEU None N
None 5 SER None N
None 6 ARG None N
None 7 LEU None N
None 8 ARG None N
None 9 LYS None N
None 10 ARG None N
None 11 GLU None N
None 12 PRO None N
None 13 ILE None N
None 14 SER None N
None 15 ILE None N
None 16 TYR None N
None 17 ASP None N
None 18 LYS None N
None 19 ILE None N
None 20 GLY None N
None 21 GLY None N
None 22 HIS None N
None 23 GLU None N
None 24 ALA None N
None 25 ILE None N
None 26 GLU None N
None 27 VAL None N
None 28 VAL None N
None 29 VAL None N
None 30 GLU None N
None 31 ASP None N
None 32 PHE None N
None 33 TYR None N
None 34 VAL None N
None 35 ARG None N
None 36 VAL None N
None 37 LEU None N
None 38 ALA None N
None 39 ASP None N
None 40 ASP None N
None 41 GLN None N
None 42 LEU None N
None 43 SER None N
None 44 ALA None N
None 45 PHE None N
None 46 PHE None N
None 47 SER None N
None 48 GLY None N
None 49 THR None N
None 50 ASN None N
None 51 MET None N
None 52 SER None N
None 53 ARG None N
None 54 LEU None N
None 55 LYS None N
None 56 GLY None N
None 57 LYS None N
None 58 GLN None N
None 59 VAL None N
None 60 GLU None N
None 61 PHE None N
None 62 PHE None N
None 63 ALA None N
None 64 ALA None N
None 65 ALA None N
None 66 LEU None N
None 67 GLY None N
None 68 GLY None N
None 69 PRO None N
None 70 GLU None N
None 71 PRO None N
None 72 TYR None N
None 73 THR None N
None 74 GLY None N
None 75 ALA None N
None 76 PRO None N
None 77 MET None N
None 78 LYS None N
None 79 GLN None N
None 80 VAL None N
None 81 HIS None N
None 82 GLN None N
None 83 GLY None N
None 84 ARG None N
None 85 GLY None N
None 86 ILE None N
None 87 THR None N
None 88 MET None N
None 89 HIS None N
None 90 HIS None N
None 91 PHE None N
None 92 SER None N
None 93 LEU None N
None 94 VAL None N
None 95 ALA None N
None 96 GLY None N
None 97 HIS None N
None 98 LEU None N
None 99 ALA None N
None 100 ASP None N
None 101 ALA None N
None 102 LEU None N
None 103 THR None N
None 104 ALA None N
None 105 ALA None N
None 106 GLY None N
None 107 VAL None N
None 108 PRO None N
None 109 SER None N
None 110 GLU None N
NoneTraceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':12@N').
111 THR None N
None 112 ILE None N
None 113 THR None N
None 114 GLU None N
None 115 ILE None N
None 116 LEU None N
None 117 GLY None N
None 118 VAL None N
None 119 ILE None N
None 120 ALA None N
None 121 PRO None N
None 122 LEU None N
None 123 ALA None N
None 124 VAL None N
None 125 ASP None N
None 126 VAL None N
None 127 THR None N
None 128 SER None N
None 129 GLY None N
None 130 GLU None N
None 131 SER None N
None 132 THR None N
None 133 THR None N
None 134 ALA None N
None 135 PRO None N
None 136 VAL None N
relax> structure.read_pdb(file='PROT-b-relax.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file 'PROT-b-relax.pdb' for reading.
Adding molecule 'PROT-b-relax_mol1' to model None (from the original molecule
number 1 of model None)
relax> structure.vectors(attached='H', spin_id=None, model=None, verbosity=1,
ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
Extracted N-H vectors for ':2@N'.
Extracted N-H vectors for ':3@N'.
Extracted N-H vectors for ':4@N'.
Extracted N-H vectors for ':5@N'.
Extracted N-H vectors for ':6@N'.
Extracted N-H vectors for ':7@N'.
Extracted N-H vectors for ':8@N'.
Extracted N-H vectors for ':9@N'.
Extracted N-H vectors for ':10@N'.
Extracted N-H vectors for ':11@N'.
Extracted N-H vectors for ':13@N'.
Extracted N-H vectors for ':14@N'.
Extracted N-H vectors for ':15@N'.
Extracted N-H vectors for ':16@N'.
Extracted N-H vectors for ':17@N'.
Extracted N-H vectors for ':18@N'.
Extracted N-H vectors for ':19@N'.
Extracted N-H vectors for ':20@N'.
Extracted N-H vectors for ':21@N'.
Extracted N-H vectors for ':22@N'.
Extracted N-H vectors for ':23@N'.
Extracted N-H vectors for ':24@N'.
Extracted N-H vectors for ':25@N'.
Extracted N-H vectors for ':26@N'.
Extracted N-H vectors for ':27@N'.
Extracted N-H vectors for ':28@N'.
Extracted N-H vectors for ':29@N'.
Extracted N-H vectors for ':30@N'.
Extracted N-H vectors for ':31@N'.
Extracted N-H vectors for ':32@N'.
Extracted N-H vectors for ':33@N'.
Extracted N-H vectors for ':34@N'.
Extracted N-H vectors for ':35@N'.
Extracted N-H vectors for ':36@N'.
Extracted N-H vectors for ':37@N'.
Extracted N-H vectors for ':38@N'.
Extracted N-H vectors for ':39@N'.
Extracted N-H vectors for ':40@N'.
Extracted N-H vectors for ':41@N'.
Extracted N-H vectors for ':42@N'.
Extracted N-H vectors for ':43@N'.
Extracted N-H vectors for ':44@N'.
Extracted N-H vectors for ':45@N'.
Extracted N-H vectors for ':46@N'.
Extracted N-H vectors for ':47@N'.
Extracted N-H vectors for ':48@N'.
Extracted N-H vectors for ':49@N'.
Extracted N-H vectors for ':50@N'.
Extracted N-H vectors for ':51@N'.
Extracted N-H vectors for ':52@N'.
Extracted N-H vectors for ':53@N'.
Extracted N-H vectors for ':54@N'.
Extracted N-H vectors for ':55@N'.
Extracted N-H vectors for ':56@N'.
Extracted N-H vectors for ':57@N'.
Extracted N-H vectors for ':58@N'.
Extracted N-H vectors for ':59@N'.
Extracted N-H vectors for ':60@N'.
Extracted N-H vectors for ':61@N'.
Extracted N-H vectors for ':62@N'.
Extracted N-H vecTraceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':69@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':71@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':76@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':108@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':121@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':135@N').
tors for ':63@N'.
Extracted N-H vectors for ':64@N'.
Extracted N-H vectors for ':65@N'.
Extracted N-H vectors for ':66@N'.
Extracted N-H vectors for ':67@N'.
Extracted N-H vectors for ':68@N'.
Extracted N-H vectors for ':70@N'.
Extracted N-H vectors for ':72@N'.
Extracted N-H vectors for ':73@N'.
Extracted N-H vectors for ':74@N'.
Extracted N-H vectors for ':75@N'.
Extracted N-H vectors for ':77@N'.
Extracted N-H vectors for ':78@N'.
Extracted N-H vectors for ':79@N'.
Extracted N-H vectors for ':80@N'.
Extracted N-H vectors for ':81@N'.
Extracted N-H vectors for ':82@N'.
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for ':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':95@N'.
Extracted N-H vectors for ':96@N'.
Extracted N-H vectors for ':97@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':100@N'.
Extracted N-H vectors for ':101@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':104@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':106@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':115@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for ':119@N'.
Extracted N-H vectors for ':120@N'.
Extracted N-H vectors for ':122@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':131@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':136@N'.
relax> relax_data.read(ri_label='R1', frq_label='800', frq=799737000.0,
file='R1-800', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R1-800' for reading.
relax> relax_data.read(ri_label='R2', frq_label='800', frq=799737000.0,
file='R2-800', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R2-800' for reading.
relax> relax_data.read(ri_label='NOE', frq_label='800', frq=799737000.0,
file='noe-800', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'noe-800' for reading.
relax> relax_data.read(ri_label='R1', frq_label='600', frq=599737000.0,
file='R1-600', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R1-600' for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=599737000.0,
file='R2-600', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R2-600' for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=599737000.0,
file='noe-600', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'noe-600' for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=499719000.0,
file='R1-500', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R1-500' for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=499719000.0,
file='R2-500', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R2-500' for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=499719000.0,
file='noe-500', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'noe-500' for reading.
relax> deselect.read(file='prolines', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, change_all=False)
Opening the file 'prolines' for reading.
relax> deselect.read(file='prolines', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, change_all=False)
Opening the file 'prolines' for reading.
relax> diffusion_tensor.copy(pipe_from='previous', pipe_to=None)
relax> fix(element='diff', fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00017199999999999998, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m0', spin_id=None)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':15&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 401.373925251
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':16&:TYR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 613.62507183
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':17&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 755.267712061
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':21&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2429.96517195
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':22&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 323.456599639
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':23&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 398.611987362
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':24&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2916.57733306
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':25&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 458.546993064
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':26&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 137.362263837
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':28&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 802.13952302
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':30&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 475.256604958
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':31&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 303.093071344
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':32&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 333.042773875
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':33&:TYR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 191.828647984
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':34&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 548.007035549
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':35&:ARG@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 228.568638502
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':36&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 338.739632868
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':37&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 151.989060326
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':43&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 3837.93182307
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':44&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2508.75740254
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':45&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2794.0796691
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':46&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1482.08367101
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':51&:MET@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 37.7067780359
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':52&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 58.7582991887
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':53&:ARG@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 364.72211635
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':55&:LYS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 639.065569148
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':56&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 447.718154178
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':58&:GLN@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1129.90927663
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':59&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 767.251962802
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':60&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 607.624335861
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':61&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 598.212858753
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':62&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 640.631011322
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':63&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 704.87070489
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':64&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 774.482634209
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':77&:MET@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 14.3361358378
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':78&:LYS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 117.555475585
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':79&:GLN@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 4491.9492783
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':80&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 540.710725847
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':81&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 331.575981704
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':90&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 260.727414013
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':91&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 619.718598016
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':92&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 379.597793635
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':93&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 542.269507967
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':94&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 428.688595
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':95&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 252.716904142
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':96&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 719.388326764
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':97&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 641.76552947
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':98&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1131.54735867
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':99&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 333.869776256
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':100&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 357.879679378
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':101&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 308.663599228
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':102&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 338.162451822
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':103&:THR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 281.989645883
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':104&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2056.63277059
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':112&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 677.230452742
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':114&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1490.74915764
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':115&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1615.88930106
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':116&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 324.21093033
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':117&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 745.955979263
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':118&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2198.33898427
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':119&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 439.066777618
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':120&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 873.385211084
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':122&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1254.73775895
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':123&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1008.5308567
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':124&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1492.93062893
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':125&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 3355.44330061
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':126&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 284.501394875
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
relax> minimise(*args=('newton',), func_tol=1e-25, max_iterations=10000000,
constraints=True, scaling=True, verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':15&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 401.373925251
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':16&:TYR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 613.62507183
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':17&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 755.267712061
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':21&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2429.96517195
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':22&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 323.456599639
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':23&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 398.611987362
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':24&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2916.57733306
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':25&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 458.546993064
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':26&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 137.362263837
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':28&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 802.13952302
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':30&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 475.256604958
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':31&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 303.093071344
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':32&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 333.042773875
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':33&:TYR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 191.828647984
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':34&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 548.007035549
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':35&:ARG@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 228.568638502
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':36&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 338.739632868
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':37&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 151.989060326
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':43&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 3837.93182307
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':44&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2508.75740254
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':45&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2794.0796691
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':46&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1482.08367101
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':51&:MET@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 37.7067780359
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':52&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 58.7582991887
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':53&:ARG@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 364.72211635
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':55&:LYS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 639.065569148
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':56&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 447.718154178
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':58&:GLN@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1129.90927663
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':59&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 767.251962802
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':60&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 607.624335861
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':61&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 598.212858753
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':62&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 640.631011322
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':63&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 704.87070489
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':64&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 774.482634209
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':77&:MET@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 14.3361358378
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':78&:LYS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 117.555475585
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':79&:GLN@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 4491.9492783
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':80&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 540.710725847
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':81&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 331.575981704
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':90&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 260.727414013
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':91&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 619.718598016
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':92&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 379.597793635
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':93&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 542.269507967
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':94&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 428.688595
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':95&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 252.716904142
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':96&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 719.388326764
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':97&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 641.76552947
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':98&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1131.54735867
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':99&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 333.869776256
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':100&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 357.879679378
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':101&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 308.663599228
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':102&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 338.162451822
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':103&:THR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 281.989645883
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':104&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2056.63277059
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':112&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 677.230452742
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':114&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1490.74915764
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':115&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1615.88930106
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':116&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 324.21093033
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':117&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 745.955979263
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':118&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2198.33898427
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':119&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 439.066777618
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':120&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 873.385211084
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':122&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1254.73775895
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':123&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1008.5308567
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':124&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1492.93062893
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':125&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 3355.44330061
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':126&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 284.501394875
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
relax> results.write(file='results', dir='sphere/round_1/m0', force=True,
compress_type=1)
Opening the file 'sphere/round_1/m0/results.bz2' for writing.
relax> pipe.create(pipe_name='m1', pipe_type='mf')
relax> sequence.read(file='1S56b_with_name.seq', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=2, sep=None)
Opening the file '1S56b_with_name.seq' for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 2 GLY None N
None 3 LEU None N
None 4 LEU None N
None 5 SER None N
None 6 ARG None N
None 7 LEU None N
None 8 ARG None N
None 9 LYS None N
None 10 ARG None N
None 11 GLU None N
None 12 PRO None N
None 13 ILE None N
None 14 SER None N
None 15 ILE None N
None 16 TYR None N
None 17 ASP None N
None 18 LYS None N
None 19 ILE None N
None 20 GLY None N
None 21 GLY None N
None 22 HIS None N
None 23 GLU None N
None 24 ALA None N
None 25 ILE None N
None 26 GLU None N
None 27 VAL None N
None 28 VAL None N
None 29 VAL None N
None 30 GLU None N
None 31 ASP None N
None 32 PHE None N
None 33 TYR None N
None 34 VAL None N
None 35 ARG None N
None 36 VAL None N
None 37 LEU None N
None 38 ALA None N
None 39 ASP None N
None 40 ASP None N
None 41 GLN None N
None 42 LEU None N
None 43 SER None N
None 44 ALA None N
None 45 PHE None N
None 46 PHE None N
None 47 SER None N
None 48 GLY None N
None 49 THR None N
None 50 ASN None N
None 51 MET None N
None 52 SER None N
None 53 ARG None N
None 54 LEU None N
None 55 LYS None N
None 56 GLY None N
None 57 LYS None N
None 58 GLN None N
None 59 VAL None N
None 60 GLU None N
None 61 PHE None N
None 62 PHE None N
None 63 ALA None N
None 64 ALA None N
None 65 ALA None N
None 66 LEU None N
None 67 GLY None N
None 68 GLY None N
None 69 PRO None N
None 70 GLU None N
None 71 PRO None N
None 72 TYR None N
None 73 THR None N
None 74 GLY None N
None 75 ALA None N
None 76 PRO None N
None 77 MET None N
None 78 LYS None N
None 79 GLN None N
None 80 VAL None N
None 81 HIS None N
None 82 GLN None N
None 83 GLY None N
None 84 ARG None N
None 85 GLY None N
None 86 ILE None N
None 87 THR None N
None 88 MET None N
None 89 HIS None N
None 90 HIS None N
None 91 PHE None N
None 92 SER None N
None 93 LEU None N
None 94 VAL None N
None 95 ALA None N
None 96 GLY None N
None 97 HIS None N
None 98 LEU None N
None 99 ALA None N
None 100 ASP None N
None 101 ALA None N
None 102 LEU None N
None 103 THR None N
None 104 ALA None N
None 105 ALA None N
None 106 GLY None N
None 107 VAL None N
None 108 PRO None N
None 109 SER None N
None 110 GLU None N
None 111 THR None N
None 112 ILE None N
None 113 THR None N
None 114 GLU None N
None 115 ILE None N
None 116 LEU None N
None 117 GLY None N
None 118 VAL None N
None 119 ILE None N
None 120 ALA None N
None 121 PRO None N
None 122 LEU None N
None 123 ALA None N
None 124 VAL None N
None 125 ASP None N
None 126 VAL None N
None 127 THR None N
None 128 SER None N
None 129 GLY None N
None 130 GLU None N
None 131 SER None N
None 132 THR None N
None Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':12@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':69@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':71@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':76@N').
133 THR None N
None 134 ALA None N
None 135 PRO None N
None 136 VAL None N
relax> structure.read_pdb(file='PROT-b-relax.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file 'PROT-b-relax.pdb' for reading.
Adding molecule 'PROT-b-relax_mol1' to model None (from the original molecule
number 1 of model None)
relax> structure.vectors(attached='H', spin_id=None, model=None, verbosity=1,
ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
Extracted N-H vectors for ':2@N'.
Extracted N-H vectors for ':3@N'.
Extracted N-H vectors for ':4@N'.
Extracted N-H vectors for ':5@N'.
Extracted N-H vectors for ':6@N'.
Extracted N-H vectors for ':7@N'.
Extracted N-H vectors for ':8@N'.
Extracted N-H vectors for ':9@N'.
Extracted N-H vectors for ':10@N'.
Extracted N-H vectors for ':11@N'.
Extracted N-H vectors for ':13@N'.
Extracted N-H vectors for ':14@N'.
Extracted N-H vectors for ':15@N'.
Extracted N-H vectors for ':16@N'.
Extracted N-H vectors for ':17@N'.
Extracted N-H vectors for ':18@N'.
Extracted N-H vectors for ':19@N'.
Extracted N-H vectors for ':20@N'.
Extracted N-H vectors for ':21@N'.
Extracted N-H vectors for ':22@N'.
Extracted N-H vectors for ':23@N'.
Extracted N-H vectors for ':24@N'.
Extracted N-H vectors for ':25@N'.
Extracted N-H vectors for ':26@N'.
Extracted N-H vectors for ':27@N'.
Extracted N-H vectors for ':28@N'.
Extracted N-H vectors for ':29@N'.
Extracted N-H vectors for ':30@N'.
Extracted N-H vectors for ':31@N'.
Extracted N-H vectors for ':32@N'.
Extracted N-H vectors for ':33@N'.
Extracted N-H vectors for ':34@N'.
Extracted N-H vectors for ':35@N'.
Extracted N-H vectors for ':36@N'.
Extracted N-H vectors for ':37@N'.
Extracted N-H vectors for ':38@N'.
Extracted N-H vectors for ':39@N'.
Extracted N-H vectors for ':40@N'.
Extracted N-H vectors for ':41@N'.
Extracted N-H vectors for ':42@N'.
Extracted N-H vectors for ':43@N'.
Extracted N-H vectors for ':44@N'.
Extracted N-H vectors for ':45@N'.
Extracted N-H vectors for ':46@N'.
Extracted N-H vectors for ':47@N'.
Extracted N-H vectors for ':48@N'.
Extracted N-H vectors for ':49@N'.
Extracted N-H vectors for ':50@N'.
Extracted N-H vectors for ':51@N'.
Extracted N-H vectors for ':52@N'.
Extracted N-H vectors for ':53@N'.
Extracted N-H vectors for ':54@N'.
Extracted N-H vectors for ':55@N'.
Extracted N-H vectors for ':56@N'.
Extracted N-H vectors for ':57@N'.
Extracted N-H vectors for ':58@N'.
Extracted N-H vectors for ':59@N'.
Extracted N-H vectors for ':60@N'.
Extracted N-H vectors for ':61@N'.
Extracted N-H vectors for ':62@N'.
Extracted N-H vectors for ':63@N'.
Extracted N-H vectors for ':64@N'.
Extracted N-H vectors for ':65@N'.
Extracted N-H vectors for ':66@N'.
Extracted N-H vectors for ':67@N'.
Extracted N-H vectors for ':68@N'.
Extracted N-H vectors for ':70@N'.
Extracted N-H vectors for ':72@N'.
Extracted N-H vectors for ':73@N'.
Extracted N-H vectors for ':74@N'.
Extracted N-H vectors for ':75@N'.
Extracted N-H vectors for ':77@N'.
Extracted N-H vectors for ':78@N'.
Extracted N-H vectors for ':79@N'.
Extracted N-H vectors for ':80@N'.
Extracted N-H vectors for ':81@N'.
Extracted N-H vectors for ':82@N'.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 364, in
vectors
bond_vectors, attached_name, warnings =
cdp.structure.bond_vectors(attached_atom=attached, model_num=model,
mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin.num,
spin_name=spin.name, return_name=True, return_warnings=True)
File "/home/pys/relax-1.3/generic_fns/structure/internal.py", line 511, in
bond_vectors
bonded_num, bonded_name, element, pos, attached_name, warnings =
self.__bonded_atom(attached_atom, index, mol)
File "/home/pys/relax-1.3/generic_fns/structure/internal.py", line 89, in
__bonded_atom
self.__find_bonded_atoms(index, mol)
File "/home/pys/relax-1.3/generic_fns/structure/internal.py", line 145, in
__find_bonded_atoms
dist = linalg.norm(centre-pos)
File "//usr/lib/python2.5/site-packages/numpy/linalg/linalg.py", line 944,
in norm
return sqrt(add.reduce((x.conj() * x).ravel().real))
KeyboardInterrupt
##############################################################################
#
#
# Copyright (C) 2004-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
# relax is free software; you can redistribute it and/or modify
#
# it under the terms of the GNU General Public License as published by
#
# the Free Software Foundation; either version 2 of the License, or
#
# (at your option) any later version.
#
#
#
# relax is distributed in the hope that it will be useful,
#
# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
# GNU General Public License for more details.
#
#
#
# You should have received a copy of the GNU General Public License
#
# along with relax; if not, write to the Free Software
#
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
#
###############################################################################
"""Script for black-box model-free analysis.
This script is designed for those who appreciate black-boxes or those who
appreciate complex code. Importantly data at multiple magnetic field
strengths is essential for this analysis. The script will need to be heavily
tailored to the molecule in question by changing the variables just below
this documentation. If you would like to change how model-free analysis is
performed, the code in the class Main can be changed as needed. For a
description of object-oriented coding in python using classes,
functions/methods, self, etc., see the python tutorial.
How to use this script
======================
The value of the variable DIFF_MODEL will determine the behaviour of this
script. The five diffusion models used in this script are:
Model I (MI) - Local tm.
Model II (MII) - Sphere.
Model III (MIII) - Prolate spheroid.
Model IV (MIV) - Oblate spheroid.
Model V (MV) - Ellipsoid.
Model I must be optimised prior to any of the other diffusion models, while
the Models II to V can be optimised in any order. To select the various
models, set the variable DIFF_MODEL to the following strings:
MI - 'local_tm'
MII - 'sphere'
MIII - 'prolate'
MIV - 'oblate'
MV - 'ellipsoid'
This approach has the advantage of eliminating the need for an initial
estimate of a global diffusion tensor and removing all the problems
associated with the initial estimate.
It is important that the number of parameters in a model does not exceed the
number of relaxation data sets for that spin. If this is the case, the list
of models in the MF_MODELS and LOCAL_TM_MODELS variables will need to be
trimmed.
Model I - Local tm
~~~~~~~~~~~~~~~~~~
This will optimise the diffusion model whereby all spin of the molecule have
a local tm value, i.e. there is no global diffusion tensor. This model needs
to be optimised prior to optimising any of the other diffusion models. Each
spin is fitted to the multiple model-free models separately, where the
parameter tm is included in each model.
AIC model selection is used to select the models for each spin.
Model II - Sphere
~~~~~~~~~~~~~~~~~
This will optimise the isotropic diffusion model. Multiple steps are
required, an initial optimisation of the diffusion tensor, followed by a
repetitive optimisation until convergence of the diffusion tensor. Each of
these steps requires this script to be rerun. For the initial optimisation,
which will be placed in the directory './sphere/init/', the following steps
are used:
The model-free models and parameter values for each spin are set to those of
diffusion model MI.
The local tm parameter is removed from the models.
The model-free parameters are fixed and a global spherical diffusion tensor
is minimised.
For the repetitive optimisation, each minimisation is named from 'round_1'
onwards. The initial 'round_1' optimisation will extract the diffusion
tensor from the results file in './sphere/init/', and the results will be
placed in the directory './sphere/round_1/'. Each successive round will take
the diffusion tensor from the previous round. The following steps are used:
The global diffusion tensor is fixed and the multiple model-free models are
fitted to each spin.
AIC model selection is used to select the models for each spin.
All model-free and diffusion parameters are allowed to vary and a global
optimisation of all parameters is carried out.
Model III - Prolate spheroid
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that
an axially symmetric diffusion tensor with Da >= 0 is used. The base
directory containing all the results is './prolate/'.
Model IV - Oblate spheroid
~~~~~~~~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that
an axially symmetric diffusion tensor with Da <= 0 is used. The base
directory containing all the results is './oblate/'.
Model V - Ellipsoid
~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that a
fully anisotropic diffusion tensor is used (also known as rhombic or
asymmetric diffusion). The base directory is './ellipsoid/'.
Final run
~~~~~~~~~
Once all the diffusion models have converged, the final run can be executed.
This is done by setting the variable DIFF_MODEL to 'final'. This consists of
two steps, diffusion tensor model selection, and Monte Carlo simulations.
Firstly AIC model selection is used to select between the diffusion tensor
models. Monte Carlo simulations are then run solely on this selected
diffusion model. Minimisation of the model is bypassed as it is assumed that
the model is already fully optimised (if this is not the case the final run
is not yet appropriate).
The final black-box model-free results will be placed in the file
'final/results'.
"""
# Python module imports.
from os import getcwd, listdir
from re import search
from string import lower
# relax module imports.
from float import floatAsByteArray
from generic_fns.mol_res_spin import generate_spin_id, spin_index_loop,
spin_loop
from generic_fns import pipes
from relax_errors import RelaxError
# User variables.
#################
# The diffusion model.
DIFF_MODEL = 'sphere'
# The model-free models (do not change these unless absolutely necessary).
MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9']
# The PDB file (set this to None if no structure is available).
PDB_FILE = 'PROT-b-relax.pdb'
# The sequence data (file name, dir, mol_name_col, res_num_col, res_name_col,
spin_num_col, spin_name_col, sep). These are the arguments to the
sequence.read() user function, for more information please see the
documentation for that function.
SEQ_ARGS = ['1S56b_with_name.seq', None, None, 0, 1, None, 2, None]
# The heteronucleus atom name corresponding to that of the PDB file (used if
the spin name is not in the sequence data).
HET_NAME = 'N'
# The relaxation data (data type, frequency label, frequency, file name, dir,
mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, sep).
These are the arguments to the relax_data.read() user function, please see
the documentation for that function for more information.
RELAX_DATA = [['R1', '800', 799.737 * 1e6, 'R1-800', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '800', 799.737 * 1e6, 'R2-800', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '800', 799.737 * 1e6, 'noe-800', None, None, 0, 1,
None, None, 2, 3, None],
['R1', '600', 599.737 * 1e6, 'R1-600', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '600', 599.737 * 1e6, 'R2-600', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '600', 599.737 * 1e6, 'noe-600', None, None, 0, 1,
None, None, 2, 3, None],
['R1', '500', 499.719 * 1e6, 'R1-500', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '500', 499.719 * 1e6, 'R2-500', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '500', 499.719 * 1e6, 'noe-500', None, None, 0, 1,
None, None, 2, 3, None]
]
# The file containing the list of unresolved spins to exclude from the
analysis (set this to None if no spin is to be excluded).
UNRES = 'prolines'
# A file containing a list of spins which can be dynamically excluded at any
point within the analysis (when set to None, this variable is not used).
EXCLUDE = 'prolines'
# The bond length, CSA values, heteronucleus type, and proton type.
BOND_LENGTH = 1.02 * 1e-10
CSA = -172 * 1e-6
HETNUC = '15N'
PROTON = '1H'
# The grid search size (the number of increments per dimension).
GRID_INC = 11
# The optimisation technique.
MIN_ALGOR = 'newton'
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
MC_NUM = 500
# Automatic looping over all rounds until convergence (must be a boolean
value of True or False).
CONV_LOOP = True
class Main:
def __init__(self, relax):
"""Execute the model-free analysis."""
# Setup.
self.relax = relax
# MI - Local tm.
################
if DIFF_MODEL == 'local_tm':
# Base directory to place files into.
self.base_dir = 'local_tm/'
# Sequential optimisation of all model-free models (function must
be modified to suit).
self.multi_model(local_tm=True)
# Model selection.
self.model_selection(modsel_pipe='aic', dir=self.base_dir + 'aic')
# Diffusion models MII to MV.
#############################
elif DIFF_MODEL == 'sphere' or DIFF_MODEL == 'prolate' or DIFF_MODEL
== 'oblate' or DIFF_MODEL == 'ellipsoid':
# Loop until convergence if CONV_LOOP is set, otherwise just loop
once.
# This looping could be made much cleaner by removing the
dependence on the determine_rnd() function.
while 1:
# Determine which round of optimisation to do (init, round_1,
round_2, etc).
self.round = self.determine_rnd(model=DIFF_MODEL)
# Inital round of optimisation for diffusion models MII to MV.
if self.round == 0:
# Base directory to place files into.
self.base_dir = DIFF_MODEL + '/init/'
# Run name.
name = DIFF_MODEL
# Create the data pipe.
pipe.create(name, 'mf')
# Load the local tm diffusion model MI results.
results.read(file='results', dir='local_tm/aic')
# Remove the tm parameter.
model_free.remove_tm()
# Deselect the spins in the EXCLUDE list.
if EXCLUDE:
deselect.read(file=EXCLUDE)
# Load the PDB file and calculate the unit vectors
parallel to the XH bond.
if PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H', spin_id='@N')
# Add an arbitrary diffusion tensor which will be
optimised.
if DIFF_MODEL == 'sphere':
diffusion_tensor.init(10e-9, fixed=False)
inc = 11
elif DIFF_MODEL == 'prolate':
diffusion_tensor.init((10e-9, 0, 0, 0),
spheroid_type='prolate', fixed=False)
inc = 11
elif DIFF_MODEL == 'oblate':
diffusion_tensor.init((10e-9, 0, 0, 0),
spheroid_type='oblate', fixed=False)
inc = 11
elif DIFF_MODEL == 'ellipsoid':
diffusion_tensor.init((10e-09, 0, 0, 0, 0, 0),
fixed=False)
inc = 6
# Minimise just the diffusion tensor.
fix('all_spins')
grid_search(inc=inc)
minimise(MIN_ALGOR)
# Write the results.
results.write(file='results', dir=self.base_dir,
force=True)
# Normal round of optimisation for diffusion models MII to MV.
else:
# Base directory to place files into.
self.base_dir = DIFF_MODEL + '/round_' + `self.round` +
'/'
# Load the optimised diffusion tensor from either the
previous round.
self.load_tensor()
# Sequential optimisation of all model-free models
(function must be modified to suit).
self.multi_model()
# Model selection.
self.model_selection(modsel_pipe='final',
dir=self.base_dir + 'aic')
# Final optimisation of all diffusion and model-free
parameters.
fix('all', fixed=False)
# Minimise all parameters.
minimise(MIN_ALGOR)
# Write the results.
dir = self.base_dir + 'opt'
results.write(file='results', dir=dir, force=True)
# Test for convergence.
converged = self.convergence()
# Break out of the infinite while loop if automatic
looping is not activated or if convergence has occurred.
if converged or not CONV_LOOP:
break
# Final run.
############
elif DIFF_MODEL == 'final':
# Diffusion model selection.
############################
# All the global diffusion models to be used in the model
selection.
self.pipes = ['local_tm', 'sphere', 'prolate', 'oblate',
'ellipsoid']
# Create the local_tm data pipe.
pipe.create('local_tm', 'mf')
# Load the local tm diffusion model MI results.
results.read(file='results', dir='local_tm/aic')
# Loop over models MII to MV.
for model in ['sphere', 'prolate', 'oblate', 'ellipsoid']:
# Determine which was the last round of optimisation for each
of the models.
self.round = self.determine_rnd(model=model) - 1
# If no directories begining with 'round_' exist, the script
has not been properly utilised!
if self.round < 1:
# Construct the name of the diffusion tensor.
name = model
if model == 'prolate' or model == 'oblate':
name = name + ' spheroid'
# Throw an error to prevent misuse of the script.
raise RelaxError, "Multiple rounds of optimisation of the
" + name + " (between 8 to 15) are required for the proper execution of this
script."
# Create the data pipe.
pipe.create(model, 'mf')
# Load the diffusion model results.
results.read(file='results', dir=model + '/round_' +
`self.round` + '/opt')
# Model selection between MI to MV.
self.model_selection(modsel_pipe='final', write_flag=False)
# Monte Carlo simulations.
##########################
# Fix the diffusion tensor, if it exists.
if hasattr(pipes.get_pipe('final'), 'diff_tensor'):
fix('diff')
# Simulations.
monte_carlo.setup(number=MC_NUM)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise(MIN_ALGOR)
eliminate()
monte_carlo.error_analysis()
# Write the final results.
##########################
results.write(file='results', dir='final', force=True)
# Unknown script behaviour.
###########################
else:
raise RelaxError, "Unknown diffusion model, change the value of
'DIFF_MODEL'"
def convergence(self):
"""Test for the convergence of the global model."""
# Alias the data pipes.
cdp = pipes.get_pipe()
prev_pipe = pipes.get_pipe('previous')
# Print out.
print "\n\n\n"
print "#####################"
print "# Convergence tests #"
print "#####################\n\n"
# Convergence flags.
chi2_converged = True
models_converged = True
params_converged = True
# Chi-squared test.
###################
print "Chi-squared test:"
print " chi2 (k-1): " + `prev_pipe.chi2`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_pipe.chi2)` + ')'
print " chi2 (k): " + `cdp.chi2`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(cdp.chi2)` + ')'
print " chi2 (difference): " + `prev_pipe.chi2 - cdp.chi2`
if prev_pipe.chi2 == cdp.chi2:
print " The chi-squared value has converged.\n"
else:
print " The chi-squared value has not converged.\n"
chi2_converged = False
# Identical model-free model test.
##################################
print "Identical model-free models test:"
# Create a string representation of the model-free models of the
previous data pipe.
prev_models = ''
for spin in spin_loop(pipe='previous'):
if hasattr(spin, 'model'):
if not spin.model == 'None':
prev_models = prev_models + spin.model
# Create a string representation of the model-free models of the
current data pipe.
curr_models = ''
for spin in spin_loop():
if hasattr(spin, 'model'):
if not spin.model == 'None':
curr_models = curr_models + spin.model
# The test.
if prev_models == curr_models:
print " The model-free models have converged.\n"
else:
print " The model-free models have not converged.\n"
models_converged = False
# Identical parameter value test.
#################################
print "Identical parameter test:"
# Only run the tests if the model-free models have converged.
if models_converged:
# Diffusion parameter array.
if DIFF_MODEL == 'sphere':
params = ['tm']
elif DIFF_MODEL == 'oblate' or DIFF_MODEL == 'prolate':
params = ['tm', 'Da', 'theta', 'phi']
elif DIFF_MODEL == 'ellipsoid':
params = ['tm', 'Da', 'Dr', 'alpha', 'beta', 'gamma']
# Tests.
for param in params:
# Get the parameter values.
prev_val = getattr(prev_pipe.diff_tensor, param)
curr_val = getattr(cdp.diff_tensor, param)
# Test if not identical.
if prev_val != curr_val:
print " Parameter: " + param
print " Value (k-1): " + `prev_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " Value (k): " + `curr_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(curr_val)` + ')'
print " The diffusion parameters have not converged.\n"
params_converged = False
# Skip the rest if the diffusion tensor parameters have not
converged.
if params_converged:
# Loop over the spins.
for mol_index, res_index, spin_index in spin_index_loop():
# Alias the spin containers.
prev_spin =
prev_pipe.mol[mol_index].res[res_index].spin[spin_index]
curr_spin =
cdp.mol[mol_index].res[res_index].spin[spin_index]
# Skip if the parameters have not converged.
if not params_converged:
break
# Skip spin systems with no 'params' object.
if not hasattr(prev_spin, 'params') or not
hasattr(curr_spin, 'params'):
continue
# The spin ID string.
spin_id =
generate_spin_id(mol_name=cdp.mol[mol_index].name,
res_num=cdp.mol[mol_index].res[res_index].num,
res_name=cdp.mol[mol_index].res[res_index].name,
spin_num=cdp.mol[mol_index].res[res_index].spin[spin_index].num,
spin_name=cdp.mol[mol_index].res[res_index].spin[spin_index].name)
# Loop over the parameters.
for j in xrange(len(curr_spin.params)):
# Get the parameter values.
prev_val = getattr(prev_spin,
lower(prev_spin.params[j]))
curr_val = getattr(curr_spin,
lower(curr_spin.params[j]))
# Test if not identical.
if prev_val != curr_val:
print " Spin ID: " + `spin_id`
print " Parameter: " + curr_spin.params[j]
print " Value (k-1): " + `prev_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " Value (k): " + `curr_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " The model-free parameters have not
converged.\n"
params_converged = False
break
# The model-free models haven't converged hence the parameter values
haven't converged.
else:
print " The model-free models haven't converged hence the
parameters haven't converged.\n"
params_converged = False
# Print out.
if params_converged:
print " The diffusion tensor and model-free parameters have
converged.\n"
# Final print out.
##################
print "\nConvergence:"
if chi2_converged and models_converged and params_converged:
print " [ Yes ]"
return True
else:
print " [ No ]"
return False
def determine_rnd(self, model=None):
"""Function for returning the name of next round of optimisation."""
# Get a list of all files in the directory model. If no directory
exists, set the round to 'init' or 0.
try:
dir_list = listdir(getcwd() + '/' + model)
except:
return 0
# Set the round to 'init' or 0 if there is no directory called 'init'.
if 'init' not in dir_list:
return 0
# Create a list of all files which begin with 'round_'.
rnd_dirs = []
for file in dir_list:
if search('^round_', file):
rnd_dirs.append(file)
# Create a sorted list of integer round numbers.
numbers = []
for dir in rnd_dirs:
try:
numbers.append(int(dir[6:]))
except:
pass
numbers.sort()
# No directories begining with 'round_' exist, set the round to 1.
if not len(numbers):
return 1
# Determine the number for the next round (add 1 to the highest
number).
return numbers[-1] + 1
def load_tensor(self):
"""Function for loading the optimised diffusion tensor."""
# Create the data pipe for the previous data (deleting the old data
pipe first if necessary).
if pipes.has_pipe('previous'):
pipe.delete('previous')
pipe.create('previous', 'mf')
# Load the optimised diffusion tensor from the initial round.
if self.round == 1:
results.read('results', DIFF_MODEL + '/init')
# Load the optimised diffusion tensor from the previous round.
else:
results.read('results', DIFF_MODEL + '/round_' + `self.round - 1`
+ '/opt')
def model_selection(self, modsel_pipe=None, dir=None, write_flag=True):
"""Model selection function."""
# Model elimination.
if modsel_pipe != 'final':
eliminate()
# Model selection (delete the model selection pipe if it already
exists).
if pipes.has_pipe(modsel_pipe):
pipe.delete(modsel_pipe)
model_selection(method='AIC', modsel_pipe=modsel_pipe,
pipes=self.pipes)
# Write the results.
if write_flag:
results.write(file='results', dir=dir, force=True)
def multi_model(self, local_tm=False):
"""Function for optimisation of all model-free models."""
# Set the data pipe names (also the names of preset model-free
models).
if local_tm:
self.pipes = LOCAL_TM_MODELS
else:
self.pipes = MF_MODELS
# Loop over the data pipes.
for name in self.pipes:
# Create the data pipe.
if pipes.has_pipe(name):
pipe.delete(name)
pipe.create(name, 'mf')
# Load the sequence.
sequence.read(SEQ_ARGS[0], SEQ_ARGS[1], SEQ_ARGS[2], SEQ_ARGS[3],
SEQ_ARGS[4], SEQ_ARGS[5], SEQ_ARGS[6], SEQ_ARGS[7])
# Name the spins if necessary.
if SEQ_ARGS[6] == None:
spin.name(HET_NAME)
# Load the PDB file and calculate the unit vectors parallel to
the XH bond.
if not local_tm and PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H')
# Load the relaxation data.
for data in RELAX_DATA:
relax_data.read(data[0], data[1], data[2], data[3], data[4],
data[5], data[6], data[7], data[8], data[9], data[10], data[11], data[12])
# Deselect spins to be excluded (including unresolved and
specifically excluded spins).
if UNRES:
deselect.read(file=UNRES)
if EXCLUDE:
deselect.read(file=EXCLUDE)
# Copy the diffusion tensor from the 'opt' data pipe and prevent
it from being minimised.
if not local_tm:
diffusion_tensor.copy('previous')
fix('diff')
# Set all the necessary values.
value.set(BOND_LENGTH, 'bond_length')
value.set(CSA, 'csa')
value.set(HETNUC, 'heteronucleus')
value.set(PROTON, 'proton')
# Select the model-free model.
model_free.select_model(model=name)
# Minimise.
grid_search(inc=GRID_INC)
minimise(MIN_ALGOR)
# Write the results.
dir = self.base_dir + name
results.write(file='results', dir=dir, force=True)
# The main class.
Main(self.relax)
[?1034h
relax repository checkout
Protein dynamics by NMR relaxation data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2009 the relax development team
This is free software which you are welcome to modify and redistribute under
the conditions of the
GNU General Public License (GPL). This program, including all modules, is
licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL'. Assistance
in using this program
can be accessed by typing 'help'.
script = 'full_analysis-sphere-error.py'
----------------------------------------------------------------------------------------------------
##############################################################################
#
#
# Copyright (C) 2004-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
# relax is free software; you can redistribute it and/or modify
#
# it under the terms of the GNU General Public License as published by
#
# the Free Software Foundation; either version 2 of the License, or
#
# (at your option) any later version.
#
#
#
# relax is distributed in the hope that it will be useful,
#
# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
# GNU General Public License for more details.
#
#
#
# You should have received a copy of the GNU General Public License
#
# along with relax; if not, write to the Free Software
#
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
#
###############################################################################
"""Script for black-box model-free analysis.
This script is designed for those who appreciate black-boxes or those who
appreciate complex code. Importantly data at multiple magnetic field
strengths is essential for this analysis. The script will need to be heavily
tailored to the molecule in question by changing the variables just below
this documentation. If you would like to change how model-free analysis is
performed, the code in the class Main can be changed as needed. For a
description of object-oriented coding in python using classes,
functions/methods, self, etc., see the python tutorial.
How to use this script
======================
The value of the variable DIFF_MODEL will determine the behaviour of this
script. The five diffusion models used in this script are:
Model I (MI) - Local tm.
Model II (MII) - Sphere.
Model III (MIII) - Prolate spheroid.
Model IV (MIV) - Oblate spheroid.
Model V (MV) - Ellipsoid.
Model I must be optimised prior to any of the other diffusion models, while
the Models II to V can be optimised in any order. To select the various
models, set the variable DIFF_MODEL to the following strings:
MI - 'local_tm'
MII - 'sphere'
MIII - 'prolate'
MIV - 'oblate'
MV - 'ellipsoid'
This approach has the advantage of eliminating the need for an initial
estimate of a global diffusion tensor and removing all the problems
associated with the initial estimate.
It is important that the number of parameters in a model does not exceed the
number of relaxation data sets for that spin. If this is the case, the list
of models in the MF_MODELS and LOCAL_TM_MODELS variables will need to be
trimmed.
Model I - Local tm
~~~~~~~~~~~~~~~~~~
This will optimise the diffusion model whereby all spin of the molecule have
a local tm value, i.e. there is no global diffusion tensor. This model needs
to be optimised prior to optimising any of the other diffusion models. Each
spin is fitted to the multiple model-free models separately, where the
parameter tm is included in each model.
AIC model selection is used to select the models for each spin.
Model II - Sphere
~~~~~~~~~~~~~~~~~
This will optimise the isotropic diffusion model. Multiple steps are
required, an initial optimisation of the diffusion tensor, followed by a
repetitive optimisation until convergence of the diffusion tensor. Each of
these steps requires this script to be rerun. For the initial optimisation,
which will be placed in the directory './sphere/init/', the following steps
are used:
The model-free models and parameter values for each spin are set to those of
diffusion model MI.
The local tm parameter is removed from the models.
The model-free parameters are fixed and a global spherical diffusion tensor
is minimised.
For the repetitive optimisation, each minimisation is named from 'round_1'
onwards. The initial 'round_1' optimisation will extract the diffusion
tensor from the results file in './sphere/init/', and the results will be
placed in the directory './sphere/round_1/'. Each successive round will take
the diffusion tensor from the previous round. The following steps are used:
The global diffusion tensor is fixed and the multiple model-free models are
fitted to each spin.
AIC model selection is used to select the models for each spin.
All model-free and diffusion parameters are allowed to vary and a global
optimisation of all parameters is carried out.
Model III - Prolate spheroid
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that
an axially symmetric diffusion tensor with Da >= 0 is used. The base
directory containing all the results is './prolate/'.
Model IV - Oblate spheroid
~~~~~~~~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that
an axially symmetric diffusion tensor with Da <= 0 is used. The base
directory containing all the results is './oblate/'.
Model V - Ellipsoid
~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that a
fully anisotropic diffusion tensor is used (also known as rhombic or
asymmetric diffusion). The base directory is './ellipsoid/'.
Final run
~~~~~~~~~
Once all the diffusion models have converged, the final run can be executed.
This is done by setting the variable DIFF_MODEL to 'final'. This consists of
two steps, diffusion tensor model selection, and Monte Carlo simulations.
Firstly AIC model selection is used to select between the diffusion tensor
models. Monte Carlo simulations are then run solely on this selected
diffusion model. Minimisation of the model is bypassed as it is assumed that
the model is already fully optimised (if this is not the case the final run
is not yet appropriate).
The final black-box model-free results will be placed in the file
'final/results'.
"""
# Python module imports.
from os import getcwd, listdir
from re import search
from string import lower
# relax module imports.
from float import floatAsByteArray
from generic_fns.mol_res_spin import generate_spin_id, spin_index_loop,
spin_loop
from generic_fns import pipes
from relax_errors import RelaxError
# User variables.
#################
# The diffusion model.
DIFF_MODEL = 'sphere'
# The model-free models (do not change these unless absolutely necessary).
MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9']
# The PDB file (set this to None if no structure is available).
PDB_FILE = 'PROT-b-relax.pdb'
# The sequence data (file name, dir, mol_name_col, res_num_col, res_name_col,
spin_num_col, spin_name_col, sep). These are the arguments to the
sequence.read() user function, for more information please see the
documentation for that function.
SEQ_ARGS = ['1S56b_with_name.seq', None, None, 0, 1, None, 2, None]
# The heteronucleus atom name corresponding to that of the PDB file (used if
the spin name is not in the sequence data).
HET_NAME = 'N'
# The relaxation data (data type, frequency label, frequency, file name, dir,
mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, sep).
These are the arguments to the relax_data.read() user function, please see
the documentation for that function for more information.
RELAX_DATA = [['R1', '800', 799.737 * 1e6, 'R1-800', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '800', 799.737 * 1e6, 'R2-800', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '800', 799.737 * 1e6, 'noe-800', None, None, 0, 1,
None, None, 2, 3, None],
['R1', '600', 599.737 * 1e6, 'R1-600', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '600', 599.737 * 1e6, 'R2-600', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '600', 599.737 * 1e6, 'noe-600', None, None, 0, 1,
None, None, 2, 3, None],
['R1', '500', 499.719 * 1e6, 'R1-500', None, None, 0, 1,
None, None, 2, 3, None],
['R2', '500', 499.719 * 1e6, 'R2-500', None, None, 0, 1,
None, None, 2, 3, None],
['NOE', '500', 499.719 * 1e6, 'noe-500', None, None, 0, 1,
None, None, 2, 3, None]
]
# The file containing the list of unresolved spins to exclude from the
analysis (set this to None if no spin is to be excluded).
UNRES = 'prolines'
# A file containing a list of spins which can be dynamically excluded at any
point within the analysis (when set to None, this variable is not used).
EXCLUDE = 'prolines'
# The bond length, CSA values, heteronucleus type, and proton type.
BOND_LENGTH = 1.02 * 1e-10
CSA = -172 * 1e-6
HETNUC = '15N'
PROTON = '1H'
# The grid search size (the number of increments per dimension).
GRID_INC = 11
# The optimisation technique.
MIN_ALGOR = 'newton'
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
MC_NUM = 500
# Automatic looping over all rounds until convergence (must be a boolean
value of True or False).
CONV_LOOP = True
class Main:
def __init__(self, relax):
"""Execute the model-free analysis."""
# Setup.
self.relax = relax
# MI - Local tm.
################
if DIFF_MODEL == 'local_tm':
# Base directory to place files into.
self.base_dir = 'local_tm/'
# Sequential optimisation of all model-free models (function must
be modified to suit).
self.multi_model(local_tm=True)
# Model selection.
self.model_selection(modsel_pipe='aic', dir=self.base_dir + 'aic')
# Diffusion models MII to MV.
#############################
elif DIFF_MODEL == 'sphere' or DIFF_MODEL == 'prolate' or DIFF_MODEL
== 'oblate' or DIFF_MODEL == 'ellipsoid':
# Loop until convergence if CONV_LOOP is set, otherwise just loop
once.
# This looping could be made much cleaner by removing the
dependence on the determine_rnd() function.
while 1:
# Determine which round of optimisation to do (init, round_1,
round_2, etc).
self.round = self.determine_rnd(model=DIFF_MODEL)
# Inital round of optimisation for diffusion models MII to MV.
if self.round == 0:
# Base directory to place files into.
self.base_dir = DIFF_MODEL + '/init/'
# Run name.
name = DIFF_MODEL
# Create the data pipe.
pipe.create(name, 'mf')
# Load the local tm diffusion model MI results.
results.read(file='results', dir='local_tm/aic')
# Remove the tm parameter.
model_free.remove_tm()
# Deselect the spins in the EXCLUDE list.
if EXCLUDE:
deselect.read(file=EXCLUDE)
# Load the PDB file and calculate the unit vectors
parallel to the XH bond.
if PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H')
# Add an arbitrary diffusion tensor which will be
optimised.
if DIFF_MODEL == 'sphere':
diffusion_tensor.init(10e-9, fixed=False)
inc = 11
elif DIFF_MODEL == 'prolate':
diffusion_tensor.init((10e-9, 0, 0, 0),
spheroid_type='prolate', fixed=False)
inc = 11
elif DIFF_MODEL == 'oblate':
diffusion_tensor.init((10e-9, 0, 0, 0),
spheroid_type='oblate', fixed=False)
inc = 11
elif DIFF_MODEL == 'ellipsoid':
diffusion_tensor.init((10e-09, 0, 0, 0, 0, 0),
fixed=False)
inc = 6
# Minimise just the diffusion tensor.
fix('all_spins')
grid_search(inc=inc)
minimise(MIN_ALGOR)
# Write the results.
results.write(file='results', dir=self.base_dir,
force=True)
# Normal round of optimisation for diffusion models MII to MV.
else:
# Base directory to place files into.
self.base_dir = DIFF_MODEL + '/round_' + `self.round` +
'/'
# Load the optimised diffusion tensor from either the
previous round.
self.load_tensor()
# Sequential optimisation of all model-free models
(function must be modified to suit).
self.multi_model()
# Model selection.
self.model_selection(modsel_pipe='final',
dir=self.base_dir + 'aic')
# Final optimisation of all diffusion and model-free
parameters.
fix('all', fixed=False)
# Minimise all parameters.
minimise(MIN_ALGOR)
# Write the results.
dir = self.base_dir + 'opt'
results.write(file='results', dir=dir, force=True)
# Test for convergence.
converged = self.convergence()
# Break out of the infinite while loop if automatic
looping is not activated or if convergence has occurred.
if converged or not CONV_LOOP:
break
# Final run.
############
elif DIFF_MODEL == 'final':
# Diffusion model selection.
############################
# All the global diffusion models to be used in the model
selection.
self.pipes = ['local_tm', 'sphere', 'prolate', 'oblate',
'ellipsoid']
# Create the local_tm data pipe.
pipe.create('local_tm', 'mf')
# Load the local tm diffusion model MI results.
results.read(file='results', dir='local_tm/aic')
# Loop over models MII to MV.
for model in ['sphere', 'prolate', 'oblate', 'ellipsoid']:
# Determine which was the last round of optimisation for each
of the models.
self.round = self.determine_rnd(model=model) - 1
# If no directories begining with 'round_' exist, the script
has not been properly utilised!
if self.round < 1:
# Construct the name of the diffusion tensor.
name = model
if model == 'prolate' or model == 'oblate':
name = name + ' spheroid'
# Throw an error to prevent misuse of the script.
raise RelaxError, "Multiple rounds of optimisation of the
" + name + " (between 8 to 15) are required for the proper execution of this
script."
# Create the data pipe.
pipe.create(model, 'mf')
# Load the diffusion model results.
results.read(file='results', dir=model + '/round_' +
`self.round` + '/opt')
# Model selection between MI to MV.
self.model_selection(modsel_pipe='final', write_flag=False)
# Monte Carlo simulations.
##########################
# Fix the diffusion tensor, if it exists.
if hasattr(pipes.get_pipe('final'), 'diff_tensor'):
fix('diff')
# Simulations.
monte_carlo.setup(number=MC_NUM)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise(MIN_ALGOR)
eliminate()
monte_carlo.error_analysis()
# Write the final results.
##########################
results.write(file='results', dir='final', force=True)
# Unknown script behaviour.
###########################
else:
raise RelaxError, "Unknown diffusion model, change the value of
'DIFF_MODEL'"
def convergence(self):
"""Test for the convergence of the global model."""
# Alias the data pipes.
cdp = pipes.get_pipe()
prev_pipe = pipes.get_pipe('previous')
# Print out.
print "\n\n\n"
print "#####################"
print "# Convergence tests #"
print "#####################\n\n"
# Convergence flags.
chi2_converged = True
models_converged = True
params_converged = True
# Chi-squared test.
###################
print "Chi-squared test:"
print " chi2 (k-1): " + `prev_pipe.chi2`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_pipe.chi2)` + ')'
print " chi2 (k): " + `cdp.chi2`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(cdp.chi2)` + ')'
print " chi2 (difference): " + `prev_pipe.chi2 - cdp.chi2`
if prev_pipe.chi2 == cdp.chi2:
print " The chi-squared value has converged.\n"
else:
print " The chi-squared value has not converged.\n"
chi2_converged = False
# Identical model-free model test.
##################################
print "Identical model-free models test:"
# Create a string representation of the model-free models of the
previous data pipe.
prev_models = ''
for spin in spin_loop(pipe='previous'):
if hasattr(spin, 'model'):
if not spin.model == 'None':
prev_models = prev_models + spin.model
# Create a string representation of the model-free models of the
current data pipe.
curr_models = ''
for spin in spin_loop():
if hasattr(spin, 'model'):
if not spin.model == 'None':
curr_models = curr_models + spin.model
# The test.
if prev_models == curr_models:
print " The model-free models have converged.\n"
else:
print " The model-free models have not converged.\n"
models_converged = False
# Identical parameter value test.
#################################
print "Identical parameter test:"
# Only run the tests if the model-free models have converged.
if models_converged:
# Diffusion parameter array.
if DIFF_MODEL == 'sphere':
params = ['tm']
elif DIFF_MODEL == 'oblate' or DIFF_MODEL == 'prolate':
params = ['tm', 'Da', 'theta', 'phi']
elif DIFF_MODEL == 'ellipsoid':
params = ['tm', 'Da', 'Dr', 'alpha', 'beta', 'gamma']
# Tests.
for param in params:
# Get the parameter values.
prev_val = getattr(prev_pipe.diff_tensor, param)
curr_val = getattr(cdp.diff_tensor, param)
# Test if not identical.
if prev_val != curr_val:
print " Parameter: " + param
print " Value (k-1): " + `prev_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " Value (k): " + `curr_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(curr_val)` + ')'
print " The diffusion parameters have not converged.\n"
params_converged = False
# Skip the rest if the diffusion tensor parameters have not
converged.
if params_converged:
# Loop over the spins.
for mol_index, res_index, spin_index in spin_index_loop():
# Alias the spin containers.
prev_spin =
prev_pipe.mol[mol_index].res[res_index].spin[spin_index]
curr_spin =
cdp.mol[mol_index].res[res_index].spin[spin_index]
# Skip if the parameters have not converged.
if not params_converged:
break
# Skip spin systems with no 'params' object.
if not hasattr(prev_spin, 'params') or not
hasattr(curr_spin, 'params'):
continue
# The spin ID string.
spin_id =
generate_spin_id(mol_name=cdp.mol[mol_index].name,
res_num=cdp.mol[mol_index].res[res_index].num,
res_name=cdp.mol[mol_index].res[res_index].name,
spin_num=cdp.mol[mol_index].res[res_index].spin[spin_index].num,
spin_name=cdp.mol[mol_index].res[res_index].spin[spin_index].name)
# Loop over the parameters.
for j in xrange(len(curr_spin.params)):
# Get the parameter values.
prev_val = getattr(prev_spin,
lower(prev_spin.params[j]))
curr_val = getattr(curr_spin,
lower(curr_spin.params[j]))
# Test if not identical.
if prev_val != curr_val:
print " Spin ID: " + `spin_id`
print " Parameter: " + curr_spin.params[j]
print " Value (k-1): " + `prev_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " Value (k): " + `curr_val`
print " (as an IEEE-754 byte array: " +
`floatAsByteArray(prev_val)` + ')'
print " The model-free parameters have not
converged.\n"
params_converged = False
break
# The model-free models haven't converged hence the parameter values
haven't converged.
else:
print " The model-free models haven't converged hence the
parameters haven't converged.\n"
params_converged = False
# Print out.
if params_converged:
print " The diffusion tensor and model-free parameters have
converged.\n"
# Final print out.
##################
print "\nConvergence:"
if chi2_converged and models_converged and params_converged:
print " [ Yes ]"
return True
else:
print " [ No ]"
return False
def determine_rnd(self, model=None):
"""Function for returning the name of next round of optimisation."""
# Get a list of all files in the directory model. If no directory
exists, set the round to 'init' or 0.
try:
dir_list = listdir(getcwd() + '/' + model)
except:
return 0
# Set the round to 'init' or 0 if there is no directory called 'init'.
if 'init' not in dir_list:
return 0
# Create a list of all files which begin with 'round_'.
rnd_dirs = []
for file in dir_list:
if search('^round_', file):
rnd_dirs.append(file)
# Create a sorted list of integer round numbers.
numbers = []
for dir in rnd_dirs:
try:
numbers.append(int(dir[6:]))
except:
pass
numbers.sort()
# No directories begining with 'round_' exist, set the round to 1.
if not len(numbers):
return 1
# Determine the number for the next round (add 1 to the highest
number).
return numbers[-1] + 1
def load_tensor(self):
"""Function for loading the optimised diffusion tensor."""
# Create the data pipe for the previous data (deleting the old data
pipe first if necessary).
if pipes.has_pipe('previous'):
pipe.delete('previous')
pipe.create('previous', 'mf')
# Load the optimised diffusion tensor from the initial round.
if self.round == 1:
results.read('results', DIFF_MODEL + '/init')
# Load the optimised diffusion tensor from the previous round.
else:
results.read('results', DIFF_MODEL + '/round_' + `self.round - 1`
+ '/opt')
def model_selection(self, modsel_pipe=None, dir=None, write_flag=True):
"""Model selection function."""
# Model elimination.
if modsel_pipe != 'final':
eliminate()
# Model selection (delete the model selection pipe if it already
exists).
if pipes.has_pipe(modsel_pipe):
pipe.delete(modsel_pipe)
model_selection(method='AIC', modsel_pipe=modsel_pipe,
pipes=self.pipes)
# Write the results.
if write_flag:
results.write(file='results', dir=dir, force=True)
def multi_model(self, local_tm=False):
"""Function for optimisation of all model-free models."""
# Set the data pipe names (also the names of preset model-free
models).
if local_tm:
self.pipes = LOCAL_TM_MODELS
else:
self.pipes = MF_MODELS
# Loop over the data pipes.
for name in self.pipes:
# Create the data pipe.
if pipes.has_pipe(name):
pipe.delete(name)
pipe.create(name, 'mf')
# Load the sequence.
sequence.read(SEQ_ARGS[0], SEQ_ARGS[1], SEQ_ARGS[2], SEQ_ARGS[3],
SEQ_ARGS[4], SEQ_ARGS[5], SEQ_ARGS[6], SEQ_ARGS[7])
# Name the spins if necessary.
if SEQ_ARGS[6] == None:
spin.name(HET_NAME)
# Load the PDB file and calculate the unit vectors parallel to
the XH bond.
if not local_tm and PDB_FILE:
structure.read_pdb(PDB_FILE)
structure.vectors(attached='H')
# Load the relaxation data.
for data in RELAX_DATA:
relax_data.read(data[0], data[1], data[2], data[3], data[4],
data[5], data[6], data[7], data[8], data[9], data[10], data[11], data[12])
# Deselect spins to be excluded (including unresolved and
specifically excluded spins).
if UNRES:
deselect.read(file=UNRES)
if EXCLUDE:
deselect.read(file=EXCLUDE)
# Copy the diffusion tensor from the 'opt' data pipe and prevent
it from being minimised.
if not local_tm:
diffusion_tensor.copy('previous')
fix('diff')
# Set all the necessary values.
value.set(BOND_LENGTH, 'bond_length')
value.set(CSA, 'csa')
value.set(HETNUC, 'heteronucleus')
value.set(PROTON, 'proton')
# Select the model-free model.
model_free.select_model(model=name)
# Minimise.
grid_search(inc=GRID_INC)
minimise(MIN_ALGOR)
# Write the results.
dir = self.base_dir + name
results.write(file='results', dir=dir, force=Traceback (most
recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':15'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':16'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':17'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':21'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':22'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':23'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':24'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':25'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':26'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':28'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':30'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':31'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':32'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':33'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':34'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':35'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':36'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':37'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':43'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':44'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':45'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':46'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':51'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':52'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':53'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':55'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':56'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':58'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':59'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':60'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':61'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':62'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':63'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':64'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':77'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':78'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':79'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':80'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':81'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':90'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':91'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':92'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':93'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':94'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':95'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':96'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':97'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':98'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':99'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':100'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':101'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':102'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':103'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':104'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':112'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':114'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':115'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':116'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':117'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':118'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':119'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':120'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':122'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':123'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':124'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':125'
to identify the corresponding atom in the molecule.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 230, in __init__
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 353, in
vectors
warn(RelaxWarning("Either the spin number or name must be set for the
spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin ':126'
to identify the corresponding atom in the molecule.
True)
# The main class.
Main(self.relax)
----------------------------------------------------------------------------------------------------
relax> pipe.create(pipe_name='sphere', pipe_type='mf')
relax> results.read(file='results', dir='local_tm/aic')
Opening the file 'local_tm/aic/results.bz2' for reading.
relax> model_free.remove_tm(spin_id=None)
relax> deselect.read(file='prolines', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, change_all=False)
Opening the file 'prolines' for reading.
relax> structure.read_pdb(file='PROT-b-relax.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file 'PROT-b-relax.pdb' for reading.
Adding molecule 'PROT-b-relax_mol1' to model None (from the original molecule
number 1 of model None)
relax> structure.vectors(attached='H', spin_id=None, model=None, verbosity=1,
ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=False)
relax> fix(element='all_spins', fixed=True)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
Only diffusion tensor parameters will be used.
Unconstrained grid search size: 11 (constraints may decrease this size).
Grid search
~~~~~~~~~~~
Searching the grid.
k: 0 xk: array([ 1000.])
fk: 1954444.19194
k: 1 xk: array([ 2100.])
fk: 1820500.71446
k: 2 xk: array([ 3200.])
fk: 1566147.00045
k: 3 xk: array([ 4300.])
fk: 1113645.19427
k: 4 xk: array([ 5400.])
fk: 718986.774228
k: 5 xk: array([ 6500.])
fk: 431715.565165
k: 6 xk: array([ 7600.])
fk: 237782.247308
k: 7 xk: array([ 8700.])
fk: 116130.130301
k: 8 xk: array([ 9800.])
fk: 50701.3406668
k: 9 xk: array([ 10900.])
fk: 30873.1176452
Parameter values: array([ 10900.])
Function value: 30873.1176452
Iterations: 11
Function calls: 11
Gradient calls: 0
Hessian calls: 0
Warning: None
relax> minimise(*args=('newton',), func_tol=1e-25, max_iterations=10000000,
constraints=True, scaling=True, verbosity=1)
Only diffusion tensor parameters will be used.
Method of Multipliers
~~~~~~~~~~~~~~~~~~~~~
k: 0 xk: array([ 10900.])
fk: 30873.1176452
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 10900.])
fk: 30873.1176452
Parameter values: array([ 10886.25622282])
Function value: 30870.1005268
Iterations: 1
Function calls: 3
Gradient calls: 2
Hessian calls: 1
Warning: None
k: 1 xk: array([ 10886.25622282])
fk: 30870.1005268
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 10886.25622282])
fk: 30870.1005268
Parameter values: array([ 10886.26769994])
Function value: 30870.1005246
Iterations: 1
Function calls: 3
Gradient calls: 2
Hessian calls: 1
Warning: None
k: 2 xk: array([ 10886.26769994])
fk: 30870.1005246
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 10886.26769994])
fk: 30870.1005246
Parameter values: array([ 10886.26769994])
Function value: 30870.1005246
Iterations: 1
Function calls: 5
Gradient calls: 2
Hessian calls: 1
Warning: None
k: 3 xk: array([ 10886.26769994])
fk: 30870.1005246
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 10886.26769994])
fk: 30870.1005246
Parameter values: array([ 10886.26769994])
Function value: 30870.1005246
Iterations: 1
Function calls: 16
Gradient calls: 2
Hessian calls: 1
Warning: None
Parameter values: array([ 10886.26769994])
Function value: 30870.1005246
Iterations: 4
Function calls: 27
Gradient calls: 8
Hessian calls: 4
Warning: None
relax> results.write(file='results', dir='sphere/init/', force=True,
compress_type=1)
Opening the file 'sphere/init//results.bz2' for writing.
relax> pipe.create(pipe_name='previous', pipe_type='mf')
relax> results.read(file='results', dir='sphere/init')
Opening the file 'sphere/init/results.bz2' for reading.
relax> pipe.create(pipe_name='m0', pipe_type='mf')
relax> sequence.read(file='1S56b_with_name.seq', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=2, sep=None)
Opening the file '1S56b_with_name.seq' for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 2 GLY None N
None 3 LEU None N
None 4 LEU None N
None 5 SER None N
None 6 ARG None N
None 7 LEU None N
None 8 ARG None N
None 9 LYS None N
None 10 ARG None N
None 11 GLU None N
None 12 PRO None N
None 13 ILE None N
None 14 SER None N
None 15 ILE None N
None 16 TYR None N
None 17 ASP None N
None 18 LYS None N
None 19 ILE None N
None 20 GLY None N
None 21 GLY None N
None 22 HIS None N
None 23 GLU None N
None 24 ALA None N
None 25 ILE None N
None 26 GLU None N
None 27 VAL None N
None 28 VAL None N
None 29 VAL None N
None 30 GLU None N
None 31 ASP None N
None 32 PHE None N
None 33 TYR None N
None 34 VAL None N
None 35 ARG None N
None 36 VAL None N
None 37 LEU None N
None 38 ALA None N
None 39 ASP None N
None 40 ASP None N
None 41 GLN None N
None 42 LEU None N
None 43 SER None N
None 44 ALA None N
None 45 PHE None N
None 46 PHE None N
None 47 SER None N
None 48 GLY None N
None 49 THR None N
None 50 ASN None N
None 51 MET None N
None 52 SER None N
None 53 ARG None N
None 54 LEU None N
None 55 LYS None N
None 56 GLY None N
None 57 LYS None N
None 58 GLN None N
None 59 VAL None N
None 60 GLU None N
None 61 PHE None N
None 62 PHE None N
None 63 ALA None N
None 64 ALA None N
None 65 ALA None N
None 66 LEU None N
None 67 GLY None N
None 68 GLY None N
None 69 PRO None N
None 70 GLU None N
None 71 PRO None N
None 72 TYR None N
None 73 THR None N
None 74 GLY None N
None 75 ALA None N
None 76 PRO None N
None 77 MET None N
None 78 LYS None N
None 79 GLN None N
None 80 VAL None N
None 81 HIS None N
None 82 GLN None N
None 83 GLY None N
None 84 ARG None N
None 85 GLY None N
None 86 ILE None N
None 87 THR None N
None 88 MET None N
None 89 HIS None N
None 90 HIS None N
None 91 PHE None N
None 92 SER None N
None 93 LEU None N
None 94 VAL None N
None 95 ALA None N
None 96 GLY None N
None 97 HIS None N
None 98 LEU None N
None 99 ALA None N
None 100 ASP None N
None 101 ALA None N
None 102 LEU None N
None 103 THR None N
None 104 ALA None N
None 105 ALA None N
None 106 GLY None N
None 107 VAL None N
None 108 PRO None N
None 109 SER None N
None 110 GLU None N
None 111 Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':12@N').
THR None N
None 112 ILE None N
None 113 THR None N
None 114 GLU None N
None 115 ILE None N
None 116 LEU None N
None 117 GLY None N
None 118 VAL None N
None 119 ILE None N
None 120 ALA None N
None 121 PRO None N
None 122 LEU None N
None 123 ALA None N
None 124 VAL None N
None 125 ASP None N
None 126 VAL None N
None 127 THR None N
None 128 SER None N
None 129 GLY None N
None 130 GLU None N
None 131 SER None N
None 132 THR None N
None 133 THR None N
None 134 ALA None N
None 135 PRO None N
None 136 VAL None N
relax> structure.read_pdb(file='PROT-b-relax.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file 'PROT-b-relax.pdb' for reading.
Adding molecule 'PROT-b-relax_mol1' to model None (from the original molecule
number 1 of model None)
relax> structure.vectors(attached='H', spin_id=None, model=None, verbosity=1,
ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
Extracted N-H vectors for ':2@N'.
Extracted N-H vectors for ':3@N'.
Extracted N-H vectors for ':4@N'.
Extracted N-H vectors for ':5@N'.
Extracted N-H vectors for ':6@N'.
Extracted N-H vectors for ':7@N'.
Extracted N-H vectors for ':8@N'.
Extracted N-H vectors for ':9@N'.
Extracted N-H vectors for ':10@N'.
Extracted N-H vectors for ':11@N'.
Extracted N-H vectors for ':13@N'.
Extracted N-H vectors for ':14@N'.
Extracted N-H vectors for ':15@N'.
Extracted N-H vectors for ':16@N'.
Extracted N-H vectors for ':17@N'.
Extracted N-H vectors for ':18@N'.
Extracted N-H vectors for ':19@N'.
Extracted N-H vectors for ':20@N'.
Extracted N-H vectors for ':21@N'.
Extracted N-H vectors for ':22@N'.
Extracted N-H vectors for ':23@N'.
Extracted N-H vectors for ':24@N'.
Extracted N-H vectors for ':25@N'.
Extracted N-H vectors for ':26@N'.
Extracted N-H vectors for ':27@N'.
Extracted N-H vectors for ':28@N'.
Extracted N-H vectors for ':29@N'.
Extracted N-H vectors for ':30@N'.
Extracted N-H vectors for ':31@N'.
Extracted N-H vectors for ':32@N'.
Extracted N-H vectors for ':33@N'.
Extracted N-H vectors for ':34@N'.
Extracted N-H vectors for ':35@N'.
Extracted N-H vectors for ':36@N'.
Extracted N-H vectors for ':37@N'.
Extracted N-H vectors for ':38@N'.
Extracted N-H vectors for ':39@N'.
Extracted N-H vectors for ':40@N'.
Extracted N-H vectors for ':41@N'.
Extracted N-H vectors for ':42@N'.
Extracted N-H vectors for ':43@N'.
Extracted N-H vectors for ':44@N'.
Extracted N-H vectors for ':45@N'.
Extracted N-H vectors for ':46@N'.
Extracted N-H vectors for ':47@N'.
Extracted N-H vectors for ':48@N'.
Extracted N-H vectors for ':49@N'.
Extracted N-H vectors for ':50@N'.
Extracted N-H vectors for ':51@N'.
Extracted N-H vectors for ':52@N'.
Extracted N-H vectors for ':53@N'.
Extracted N-H vectors for ':54@N'.
Extracted N-H vectors for ':55@N'.
Extracted N-H vectors for ':56@N'.
Extracted N-H vectors for ':57@N'.
Extracted N-H vectors for ':58@N'.
Extracted N-H vectors for ':59@N'.
Extracted N-H vectors for ':60@N'.
Extracted N-H vectors for ':61@N'.
Extracted N-H vectors for ':62@N'.
Extracted N-H vectors for ':63@Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':69@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':71@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':76@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':108@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':121@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':135@N').
N'.
Extracted N-H vectors for ':64@N'.
Extracted N-H vectors for ':65@N'.
Extracted N-H vectors for ':66@N'.
Extracted N-H vectors for ':67@N'.
Extracted N-H vectors for ':68@N'.
Extracted N-H vectors for ':70@N'.
Extracted N-H vectors for ':72@N'.
Extracted N-H vectors for ':73@N'.
Extracted N-H vectors for ':74@N'.
Extracted N-H vectors for ':75@N'.
Extracted N-H vectors for ':77@N'.
Extracted N-H vectors for ':78@N'.
Extracted N-H vectors for ':79@N'.
Extracted N-H vectors for ':80@N'.
Extracted N-H vectors for ':81@N'.
Extracted N-H vectors for ':82@N'.
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for ':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':95@N'.
Extracted N-H vectors for ':96@N'.
Extracted N-H vectors for ':97@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':100@N'.
Extracted N-H vectors for ':101@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':104@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':106@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':115@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for ':119@N'.
Extracted N-H vectors for ':120@N'.
Extracted N-H vectors for ':122@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':131@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':136@N'.
relax> relax_data.read(ri_label='R1', frq_label='800', frq=799737000.0,
file='R1-800', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R1-800' for reading.
relax> relax_data.read(ri_label='R2', frq_label='800', frq=799737000.0,
file='R2-800', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R2-800' for reading.
relax> relax_data.read(ri_label='NOE', frq_label='800', frq=799737000.0,
file='noe-800', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'noe-800' for reading.
relax> relax_data.read(ri_label='R1', frq_label='600', frq=599737000.0,
file='R1-600', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R1-600' for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=599737000.0,
file='R2-600', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R2-600' for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=599737000.0,
file='noe-600', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'noe-600' for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=499719000.0,
file='R1-500', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R1-500' for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=499719000.0,
file='R2-500', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R2-500' for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=499719000.0,
file='noe-500', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'noe-500' for reading.
relax> deselect.read(file='prolines', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, change_all=False)
Opening the file 'prolines' for reading.
relax> deselect.read(file='prolines', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, change_all=False)
Opening the file 'prolines' for reading.
relax> diffusion_tensor.copy(pipe_from='previous', pipe_to=None)
relax> fix(element='diff', fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00017199999999999998, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m0', spin_id=None)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':15&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 401.373925251
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':16&:TYR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 613.62507183
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':17&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 755.267712061
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':21&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2429.96517195
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':22&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 323.456599639
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':23&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 398.611987362
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':24&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2916.57733306
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':25&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 458.546993064
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':26&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 137.362263837
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':28&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 802.13952302
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':30&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 475.256604958
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':31&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 303.093071344
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':32&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 333.042773875
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':33&:TYR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 191.828647984
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':34&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 548.007035549
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':35&:ARG@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 228.568638502
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':36&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 338.739632868
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':37&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 151.989060326
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':43&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 3837.93182307
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':44&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2508.75740254
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':45&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2794.0796691
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':46&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1482.08367101
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':51&:MET@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 37.7067780359
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':52&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 58.7582991887
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':53&:ARG@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 364.72211635
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':55&:LYS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 639.065569148
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':56&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 447.718154178
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':58&:GLN@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1129.90927663
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':59&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 767.251962802
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':60&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 607.624335861
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':61&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 598.212858753
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':62&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 640.631011322
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':63&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 704.87070489
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':64&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 774.482634209
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':77&:MET@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 14.3361358378
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':78&:LYS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 117.555475585
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':79&:GLN@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 4491.9492783
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':80&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 540.710725847
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':81&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 331.575981704
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':90&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 260.727414013
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':91&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 619.718598016
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':92&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 379.597793635
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':93&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 542.269507967
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':94&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 428.688595
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':95&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 252.716904142
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':96&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 719.388326764
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':97&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 641.76552947
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':98&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1131.54735867
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':99&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 333.869776256
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':100&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 357.879679378
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':101&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 308.663599228
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':102&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 338.162451822
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':103&:THR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 281.989645883
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':104&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2056.63277059
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':112&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 677.230452742
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':114&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1490.74915764
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':115&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1615.88930106
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':116&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 324.21093033
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':117&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 745.955979263
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':118&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2198.33898427
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':119&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 439.066777618
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':120&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 873.385211084
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':122&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1254.73775895
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':123&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1008.5308567
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':124&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1492.93062893
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':125&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 3355.44330061
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':126&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 1 (constraints may decrease this size).
Cannot run a grid search on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 284.501394875
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
relax> minimise(*args=('newton',), func_tol=1e-25, max_iterations=10000000,
constraints=True, scaling=True, verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':15&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 401.373925251
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':16&:TYR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 613.62507183
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':17&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 755.267712061
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':21&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2429.96517195
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':22&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 323.456599639
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':23&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 398.611987362
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':24&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2916.57733306
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':25&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 458.546993064
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':26&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 137.362263837
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':28&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 802.13952302
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':30&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 475.256604958
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':31&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 303.093071344
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':32&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 333.042773875
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':33&:TYR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 191.828647984
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':34&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 548.007035549
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':35&:ARG@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 228.568638502
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':36&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 338.739632868
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':37&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 151.989060326
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':43&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 3837.93182307
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':44&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2508.75740254
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':45&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2794.0796691
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':46&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1482.08367101
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':51&:MET@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 37.7067780359
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':52&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 58.7582991887
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':53&:ARG@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 364.72211635
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':55&:LYS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 639.065569148
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':56&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 447.718154178
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':58&:GLN@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1129.90927663
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':59&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 767.251962802
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':60&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 607.624335861
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':61&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 598.212858753
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':62&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 640.631011322
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':63&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 704.87070489
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':64&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 774.482634209
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':77&:MET@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 14.3361358378
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':78&:LYS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 117.555475585
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':79&:GLN@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 4491.9492783
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':80&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 540.710725847
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':81&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 331.575981704
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':90&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 260.727414013
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':91&:PHE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 619.718598016
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':92&:SER@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 379.597793635
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':93&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 542.269507967
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':94&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 428.688595
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':95&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 252.716904142
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':96&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 719.388326764
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':97&:HIS@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 641.76552947
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':98&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1131.54735867
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':99&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 333.869776256
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':100&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 357.879679378
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':101&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 308.663599228
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':102&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 338.162451822
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':103&:THR@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 281.989645883
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':104&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2056.63277059
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':112&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 677.230452742
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':114&:GLU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1490.74915764
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':115&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1615.88930106
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':116&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 324.21093033
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':117&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 745.955979263
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':118&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 2198.33898427
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':119&:ILE@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 439.066777618
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':120&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 873.385211084
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':122&:LEU@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1254.73775895
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':123&:ALA@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1008.5308567
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':124&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 1492.93062893
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':125&:ASP@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 3355.44330061
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
Fitting to spin ':126&:VAL@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cannot run optimisation on a model with zero parameters.
Directly calculating the function value.
Parameter values: array([], dtype=float64)
Function value: 284.501394875
Iterations: 0
Function calls: 1
Gradient calls: 0
Hessian calls: 0
Warning: No optimisation
relax> results.write(file='results', dir='sphere/round_1/m0', force=True,
compress_type=1)
Opening the file 'sphere/round_1/m0/results.bz2' for writing.
relax> pipe.create(pipe_name='m1', pipe_type='mf')
relax> sequence.read(file='1S56b_with_name.seq', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=2, sep=None)
Opening the file '1S56b_with_name.seq' for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 2 GLY None N
None 3 LEU None N
None 4 LEU None N
None 5 SER None N
None 6 ARG None N
None 7 LEU None N
None 8 ARG None N
None 9 LYS None N
None 10 ARG None N
None 11 GLU None N
None 12 PRO None N
None 13 ILE None N
None 14 SER None N
None 15 ILE None N
None 16 TYR None N
None 17 ASP None N
None 18 LYS None N
None 19 ILE None N
None 20 GLY None N
None 21 GLY None N
None 22 HIS None N
None 23 GLU None N
None 24 ALA None N
None 25 ILE None N
None 26 GLU None N
None 27 VAL None N
None 28 VAL None N
None 29 VAL None N
None 30 GLU None N
None 31 ASP None N
None 32 PHE None N
None 33 TYR None N
None 34 VAL None N
None 35 ARG None N
None 36 VAL None N
None 37 LEU None N
None 38 ALA None N
None 39 ASP None N
None 40 ASP None N
None 41 GLN None N
None 42 LEU None N
None 43 SER None N
None 44 ALA None N
None 45 PHE None N
None 46 PHE None N
None 47 SER None N
None 48 GLY None N
None 49 THR None N
None 50 ASN None N
None 51 MET None N
None 52 SER None N
None 53 ARG None N
None 54 LEU None N
None 55 LYS None N
None 56 GLY None N
None 57 LYS None N
None 58 GLN None N
None 59 VAL None N
None 60 GLU None N
None 61 PHE None N
None 62 PHE None N
None 63 ALA None N
None 64 ALA None N
None 65 ALA None N
None 66 LEU None N
None 67 GLY None N
None 68 GLY None N
None 69 PRO None N
None 70 GLU None N
None 71 PRO None N
None 72 TYR None N
None 73 THR None N
None 74 GLY None N
None 75 ALA None N
None 76 PRO None N
None 77 MET None N
None 78 LYS None N
None 79 GLN None N
None 80 VAL None N
None 81 HIS None N
None 82 GLN None N
None 83 GLY None N
None 84 ARG None N
None 85 GLY None N
None 86 ILE None N
None 87 THR None N
None 88 MET None N
None 89 HIS None N
None 90 HIS None N
None 91 PHE None N
None 92 SER None N
None 93 LEU None N
None 94 VAL None N
None 95 ALA None N
None 96 GLY None N
None 97 HIS None N
None 98 LEU None N
None 99 ALA None N
None 100 ASP None N
None 101 ALA None N
None 102 LEU None N
None 103 THR None N
None 104 ALA None N
None 105 ALA None N
None 106 GLY None N
None 107 VAL None N
None 108 PRO None N
None 109 SER None N
None 110 GLU None N
None 111 THR None N
None 112 ILE None N
None 113 THR None N
None 114 GLU None N
None 115 ILE None N
None 116 LEU None N
None 117 GLY None N
None 118 VAL None N
None 119 ILE None N
None 120 ALA None N
None 121 PRO None N
None 122 LEU None N
None 123 ALA None N
None 124 VAL None N
None 125 ASP None N
None 126 VAL None N
None 127 THR None N
None 128 SER None N
None 129 GLY None N
None 130 GLU None N
None 131 SER None N
None 132 THR None N
None 133 THRTraceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':12@N').
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 370, in
vectors
warn(RelaxWarning(warnings + " (atom ID " + `id` + ")."))
RelaxWarning: No attached atom could be found (atom ID ':69@N').
None N
None 134 ALA None N
None 135 PRO None N
None 136 VAL None N
relax> structure.read_pdb(file='PROT-b-relax.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file 'PROT-b-relax.pdb' for reading.
Adding molecule 'PROT-b-relax_mol1' to model None (from the original molecule
number 1 of model None)
relax> structure.vectors(attached='H', spin_id=None, model=None, verbosity=1,
ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
Extracted N-H vectors for ':2@N'.
Extracted N-H vectors for ':3@N'.
Extracted N-H vectors for ':4@N'.
Extracted N-H vectors for ':5@N'.
Extracted N-H vectors for ':6@N'.
Extracted N-H vectors for ':7@N'.
Extracted N-H vectors for ':8@N'.
Extracted N-H vectors for ':9@N'.
Extracted N-H vectors for ':10@N'.
Extracted N-H vectors for ':11@N'.
Extracted N-H vectors for ':13@N'.
Extracted N-H vectors for ':14@N'.
Extracted N-H vectors for ':15@N'.
Extracted N-H vectors for ':16@N'.
Extracted N-H vectors for ':17@N'.
Extracted N-H vectors for ':18@N'.
Extracted N-H vectors for ':19@N'.
Extracted N-H vectors for ':20@N'.
Extracted N-H vectors for ':21@N'.
Extracted N-H vectors for ':22@N'.
Extracted N-H vectors for ':23@N'.
Extracted N-H vectors for ':24@N'.
Extracted N-H vectors for ':25@N'.
Extracted N-H vectors for ':26@N'.
Extracted N-H vectors for ':27@N'.
Extracted N-H vectors for ':28@N'.
Extracted N-H vectors for ':29@N'.
Extracted N-H vectors for ':30@N'.
Extracted N-H vectors for ':31@N'.
Extracted N-H vectors for ':32@N'.
Extracted N-H vectors for ':33@N'.
Extracted N-H vectors for ':34@N'.
Extracted N-H vectors for ':35@N'.
Extracted N-H vectors for ':36@N'.
Extracted N-H vectors for ':37@N'.
Extracted N-H vectors for ':38@N'.
Extracted N-H vectors for ':39@N'.
Extracted N-H vectors for ':40@N'.
Extracted N-H vectors for ':41@N'.
Extracted N-H vectors for ':42@N'.
Extracted N-H vectors for ':43@N'.
Extracted N-H vectors for ':44@N'.
Extracted N-H vectors for ':45@N'.
Extracted N-H vectors for ':46@N'.
Extracted N-H vectors for ':47@N'.
Extracted N-H vectors for ':48@N'.
Extracted N-H vectors for ':49@N'.
Extracted N-H vectors for ':50@N'.
Extracted N-H vectors for ':51@N'.
Extracted N-H vectors for ':52@N'.
Extracted N-H vectors for ':53@N'.
Extracted N-H vectors for ':54@N'.
Extracted N-H vectors for ':55@N'.
Extracted N-H vectors for ':56@N'.
Extracted N-H vectors for ':57@N'.
Extracted N-H vectors for ':58@N'.
Extracted N-H vectors for ':59@N'.
Extracted N-H vectors for ':60@N'.
Extracted N-H vectors for ':61@N'.
Extracted N-H vectors for ':62@N'.
Extracted N-H vectors for ':63@N'.
Extracted N-H vectors for ':64@N'.
Extracted N-H vectors for ':65@N'.
Extracted N-H vectors for ':66@N'.
Extracted N-H vectors for ':67@N'.
Extracted N-H vectors for ':68@N'.
Traceback (most recent call last):
File "/home/pys/relax-1.3/relax", line 418, in <module>
Relax()
File "/home/pys/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 273, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 534, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/pys/relax-1.3/prompt/interpreter.py", line 430, in
interact_script
execfile(script_file, local)
File "full_analysis-sphere-error.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere-error.py", line 264, in __init__
self.multi_model()
File "full_analysis-sphere-error.py", line 605, in multi_model
structure.vectors(attached='H')
File "/home/pys/relax-1.3/prompt/structure.py", line 586, in vectors
generic_fns.structure.main.vectors(attached=attached, spin_id=spin_id,
model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/home/pys/relax-1.3/generic_fns/structure/main.py", line 364, in
vectors
bond_vectors, attached_name, warnings =
cdp.structure.bond_vectors(attached_atom=attached, model_num=model,
mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin.num,
spin_name=spin.name, return_name=True, return_warnings=True)
File "/home/pys/relax-1.3/generic_fns/structure/internal.py", line 511, in
bond_vectors
bonded_num, bonded_name, element, pos, attached_name, warnings =
self.__bonded_atom(attached_atom, index, mol)
File "/home/pys/relax-1.3/generic_fns/structure/internal.py", line 89, in
__bonded_atom
self.__find_bonded_atoms(index, mol)
File "/home/pys/relax-1.3/generic_fns/structure/internal.py", line 148, in
__find_bonded_atoms
if dist < radius:
KeyboardInterrupt
Re: full_analysys problem: 'All parameters are fixed'