Hi, Edward,
Thanks, as your instruction, I tried Gui, but I could not quit selection
relaxation dispersion models. (I just report as a bug)
1) In r2eff_read, I am not quite clear about the pop window. You said I
should load partial experiment ID string as ('%s_%s'%(id,dis_point)).
Then you have the second window to load the file. what does the file
mean? The file is the fitted R2eff or a list for all the R2eff file names?
Is that possible to load a series of files? I guess so, but do you have
an example somewhere?
2) actually, I found script is more powerful, so I just use Troels
mentioned trick. type help(relax_disp.r2eff), then I found the
description about this function.
I made one script, it is included in the log file.
I attached the log file after I run the script.You can see that it reads
all the R2eff value perfectly, but did not do the calculation there.
It is a bit strange to me. . Do you have an idea why?
Do not care too much about the value in the script, such as Grid_inc,
MC_value, they are only for test now.
Peixiang
On 05/30/2014 04:45 PM, Edward d'Auvergne wrote:
Hi Peixiang,
If you do only have R2eff data, i.e. there is no original peak lists,
I'll assume that you would fit into the category of 'power user'. In
this case in the GUI, instead of using the peak intensity wizard via
the spectra list 'Add' button, try the "User
functions->relax_disp->r2eff_read" or "User
functions->relax_disp->r2eff_read_spin" menu entries. You will have
to deselect the 'R2eff' model. Clicking on the 'Execute' button will
then run the analysis.
Regards,
Edward
--
Peixiang Ma, PhD.
Institut de Biologie Structurale (IBS)
UMR 5075 - CEA - CNRS - UJF
41 rue Jules Horowitz
38027 Grenoble Cedex 1, France
Email: Peixiang.Ma@xxxxxx
relax 3.2.1
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2014 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' within the
relax prompt.
Assistance in using the relax prompt and scripting interface can be accessed
by typing 'help' within
the prompt.
Processor fabric: Uni-processor.
script = 'R1rho_analysis_R2eff_PX.py'
----------------------------------------------------------------------------------------------------
###############################################################################
#
#
# Copyright (C) 2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
# This program 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 3 of the License, or
#
# (at your option) any later version.
#
#
#
# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
#
#
#
###############################################################################
"""Script for performing a full relaxation dispersion analysis using
off-resonance R1rho-type data."""
# Python module imports.
from os import sep
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
# Analysis variables.
#####################
# The dispersion models.
MODELS = ['MP05','NS R1rho 2-site']#, 'No Rex', 'R2eff',
# The grid search size (the number of increments per dimension).
GRID_INC = 11
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
MC_NUM = 3
# A flag which if True will activate Monte Carlo simulations for all models.
Note this will hugely increase the computation time.
MC_SIM_ALL_MODELS = False
# The results directory.
RESULTS_DIR = './test_R1rho_R2eff/'
# The directory of results of an earlier analysis without clustering.
PRE_RUN_DIR = None
# The model selection technique to use.
MODSEL = 'AIC'
# The flag for only using numeric models in the final model selection.
NUMERIC_ONLY = False
# The R1rho value in rad/s by which to judge insignificance. If the maximum
difference between two points on all dispersion curves for a spin is less
than this value, that spin will be deselected.
INSIGNIFICANCE = 1.0
# Set up the data pipe.
#######################
# The path to the data files.
DATA_PATH='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax'
# Create the data pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
# Load the sequence.
sequence.read('1UBQ_sel.seq', dir=DATA_PATH, res_num_col=2, res_name_col=3)
# Name the spins so they can be matched to the assignments.
spin.name(name='N')
# Set the isotope information.
spin.isotope(isotope='15N')
# The spectral data - spectrum ID, peak lists, offset frequency (Hz),
relaxation time period (s), baseplane RMSD estimate.
data = []
spin_lock = [2000, 2506, 2987, 4000, 4987, 6000, 7493, 10000,12506,14987]
for spin_lock_index in range(len(spin_lock)):
data.append(["nu_%s" % (spin_lock[spin_lock_index]),
"nu_%s_600MHz.list" % (spin_lock[spin_lock_index]),
spin_lock[spin_lock_index], 2.0])
print data
# Loop over the spectral data, loading it and setting the metadata.
for i in range(len(data)):
# Set the relaxation dispersion experiment type.
relax_disp.exp_type(spectrum_id=data[i][0], exp_type='R1rho')
# Set the spin-lock offset.the spin-lock offset (ppm)
relax_disp.spin_lock_offset(spectrum_id=data[i][0], offset=117)
# Set the relaxation dispersion spin-lock field strength (nu1).
relax_disp.spin_lock_field(spectrum_id=data[i][0], field=data[i][2])
# Set the spectrometer frequency.
spectrometer.frequency(id=data[i][0], frq=600.2, units='MHz')
relax_disp.r2eff_read(file=data[i][1],dir=DATA_PATH,
id=data[i][0],disp_frq=data[i][2], mol_name_col=1, res_num_col=2,
res_name_col=3, data_col=4, error_col=5)
# Load the R1 data.
relax_data.read(ri_id='600MHz', ri_type='R1', frq=600.2e6, file='R1.out',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
# Clustering (only to be activated after an initial analysis without
clustering).
#relax_disp.cluster(cluster_id='cluster', spin_id=':1-50')
# Read the chemical shift data.
chemical_shift.read(file='nu_2000_ncyc1.list', dir=DATA_PATH)
# Deselect unresolved spins.
#deselect.read(file='unresolved', dir=DATA_PATH, res_num_col=1)
# Auto-analysis execution.
##########################
# Do not change!
Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM,
modsel=MODSEL, pre_run_dir=PRE_RUN_DIR, insignificance=INSIGNIFICANCE,
numeric_only=NUMERIC_ONLY, mc_sim_all_models=MC_SIM_ALL_MODELS)
----------------------------------------------------------------------------------------------------
relax> pipe.create(pipe_name='base pipe', pipe_type='relax_disp',
bundle='relax_disp')
relax> sequence.read(file='1UBQ_sel.seq',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
spin_id_col=None, mol_name_col=None, res_num_col=2, res_name_col=3,
spin_num_col=None, spin_name_col=None, sep=None, spin_id=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/1UBQ_sel.seq'
for reading.
# mol_name res_num res_name spin_num spin_name
None 23 Trp None None
None 27 Trp None None
None 51 Trp None None
None 52 Trp None None
None 54 Trp None None
None 55 Trp None None
relax> spin.name(name='N', spin_id=None, force=False)
relax> spin.isotope(isotope='15N', spin_id=None, force=False)
[['nu_2000', 'nu_2000_600MHz.list', 2000, 2.0], ['nu_2506',
'nu_2506_600MHz.list', 2506, 2.0], ['nu_2987', 'nu_2987_600MHz.list', 2987,
2.0], ['nu_4000', 'nu_4000_600MHz.list', 4000, 2.0], ['nu_4987',
'nu_4987_600MHz.list', 4987, 2.0], ['nu_6000', 'nu_6000_600MHz.list', 6000,
2.0], ['nu_7493', 'nu_7493_600MHz.list', 7493, 2.0], ['nu_10000',
'nu_10000_600MHz.list', 10000, 2.0], ['nu_12506', 'nu_12506_600MHz.list',
12506, 2.0], ['nu_14987', 'nu_14987_600MHz.list', 14987, 2.0]]
relax> relax_disp.exp_type(spectrum_id='nu_2000', exp_type='R1rho')
The spectrum ID 'nu_2000' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_2000', offset=117)
Setting the 'nu_2000' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_2000', field=2000)
The spectrum ID 'nu_2000' spin-lock field strength is set to 2.0 kHz.
relax> spectrometer.frequency(id='nu_2000', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_2000', file='nu_2000_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=2000, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_2000_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
7.47088981965 0.775500836124
None 52 Trp None None
10.411019349 1.20865813721
None 27 Trp None None
3.76253358823 0.54581421379
None 23 Trp None None
8.13046221134 0.647923249516
None 51 Trp None None
10.9324835609 1.171793768
None 55 Trp None None
5.98098032361 0.735026341414
The spectrum ID 'nu_2000' spin-lock field strength is set to 2.0 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_2506', exp_type='R1rho')
The spectrum ID 'nu_2506' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_2506', offset=117)
Setting the 'nu_2506' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_2506', field=2506)
The spectrum ID 'nu_2506' spin-lock field strength is set to 2.506 kHz.
relax> spectrometer.frequency(id='nu_2506', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_2506', file='nu_2506_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=2506, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_2506_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
7.03840380274 0.793125644404
None 52 Trp None None
10.2109676534 1.10523008129
None 27 Trp None None
3.46664782932 0.584465651858
None 23 Trp None None
6.57381645123 0.494165794933
None 51 Trp None None
9.39953660135 0.914321198048
None 55 Trp None None
6.07143090552 0.610061240509
The spectrum ID 'nu_2506' spin-lock field strength is set to 2.506 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_2987', exp_type='R1rho')
The spectrum ID 'nu_2987' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_2987', offset=117)
Setting the 'nu_2987' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_2987', field=2987)
The spectrum ID 'nu_2987' spin-lock field strength is set to 2.987 kHz.
relax> spectrometer.frequency(id='nu_2987', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_2987', file='nu_2987_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=2987, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_2987_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
6.80188276619 0.761988220361
None 52 Trp None None
9.97052319504 0.963502763958
None 27 Trp None None
3.51404638409 0.65891313492
None 23 Trp None None
5.77100146957 0.505471221495
None 51 Trp None None
9.13610317046 0.837063782912
None 55 Trp None None
5.71516082316 0.590598272578
The spectrum ID 'nu_2987' spin-lock field strength is set to 2.987 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_4000', exp_type='R1rho')
The spectrum ID 'nu_4000' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_4000', offset=117)
Setting the 'nu_4000' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_4000', field=4000)
The spectrum ID 'nu_4000' spin-lock field strength is set to 4.0 kHz.
relax> spectrometer.frequency(id='nu_4000', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_4000', file='nu_4000_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=4000, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_4000_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
5.87138217495 0.609634300499
None 52 Trp None None
9.5423216384 0.956353493834
None 27 Trp None None
3.61243807814 0.586809165979
None 23 Trp None None
4.82525323599 0.419000481897
None 51 Trp None None
7.46557640126 0.700457484815
None 55 Trp None None
5.49054669371 0.491371650144
The spectrum ID 'nu_4000' spin-lock field strength is set to 4.0 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_4987', exp_type='R1rho')
The spectrum ID 'nu_4987' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_4987', offset=117)
Setting the 'nu_4987' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_4987', field=4987)
The spectrum ID 'nu_4987' spin-lock field strength is set to 4.987 kHz.
relax> spectrometer.frequency(id='nu_4987', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_4987', file='nu_4987_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=4987, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_4987_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
5.77248042547 0.564613726748
None 52 Trp None None
8.8786807016 0.785803048162
None 27 Trp None None
2.96642166679 0.549920389748
None 23 Trp None None
4.05217798455 0.346331119976
None 51 Trp None None
7.251431117 0.727981085534
None 55 Trp None None
4.87386383801 0.490188582691
The spectrum ID 'nu_4987' spin-lock field strength is set to 4.987 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_6000', exp_type='R1rho')
The spectrum ID 'nu_6000' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_6000', offset=117)
Setting the 'nu_6000' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_6000', field=6000)
The spectrum ID 'nu_6000' spin-lock field strength is set to 6.0 kHz.
relax> spectrometer.frequency(id='nu_6000', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_6000', file='nu_6000_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=6000, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_6000_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
5.59437071791 0.538989857477
None 52 Trp None None
8.77151919303 0.877580230943
None 27 Trp None None
2.8393406904 0.549249477975
None 23 Trp None None
3.72221322473 0.323737395424
None 51 Trp None None
6.74866317349 0.564109709966
None 55 Trp None None
4.73830561787 0.432964327421
The spectrum ID 'nu_6000' spin-lock field strength is set to 6.0 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_7493', exp_type='R1rho')
The spectrum ID 'nu_7493' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_7493', offset=117)
Setting the 'nu_7493' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_7493', field=7493)
The spectrum ID 'nu_7493' spin-lock field strength is set to 7.493 kHz.
relax> spectrometer.frequency(id='nu_7493', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_7493', file='nu_7493_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=7493, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_7493_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
5.48022151986 0.478826714017
None 52 Trp None None
9.16913959244 0.862969698079
None 27 Trp None None
2.91464982184 0.478473940565
None 23 Trp None None
3.50353564249 0.303192359214
None 51 Trp None None
6.24357862604 0.572673053645
None 55 Trp None None
4.70895274076 0.389897621795
The spectrum ID 'nu_7493' spin-lock field strength is set to 7.493 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_10000', exp_type='R1rho')
The spectrum ID 'nu_10000' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_10000', offset=117)
Setting the 'nu_10000' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_10000', field=10000)
The spectrum ID 'nu_10000' spin-lock field strength is set to 10.0 kHz.
relax> spectrometer.frequency(id='nu_10000', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_10000', file='nu_10000_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=10000, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_10000_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
5.55214859199 0.552581302566
None 52 Trp None None
7.94503475148 0.72370527931
None 27 Trp None None
2.8158912864 0.582095129718
None 23 Trp None None
3.07735271251 0.35645462317
None 51 Trp None None
6.5014178036 0.642724587375
None 55 Trp None None
4.58916456446 0.489579114425
The spectrum ID 'nu_10000' spin-lock field strength is set to 10.0 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_12506', exp_type='R1rho')
The spectrum ID 'nu_12506' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_12506', offset=117)
Setting the 'nu_12506' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_12506', field=12506)
The spectrum ID 'nu_12506' spin-lock field strength is set to 12.506 kHz.
relax> spectrometer.frequency(id='nu_12506', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_12506', file='nu_12506_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=12506, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_12506_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
5.45388272223 0.593251366761
None 52 Trp None None
8.4375682003 0.833242361108
None 27 Trp None None
2.52333845194 0.54085243
None 23 Trp None None
2.83589565885 0.345896901906
None 51 Trp None None
5.94510764434 0.558546717414
None 55 Trp None None
4.35468952709 0.402950328465
The spectrum ID 'nu_12506' spin-lock field strength is set to 12.506 kHz.
relax> relax_disp.exp_type(spectrum_id='nu_14987', exp_type='R1rho')
The spectrum ID 'nu_14987' is now set to the R1rho-type experiment.
relax> relax_disp.spin_lock_offset(spectrum_id='nu_14987', offset=117)
Setting the 'nu_14987' spectrum spin-lock offset to 117.0 ppm.
relax> relax_disp.spin_lock_field(spectrum_id='nu_14987', field=14987)
The spectrum ID 'nu_14987' spin-lock field strength is set to 14.987 kHz.
relax> spectrometer.frequency(id='nu_14987', frq=600.2, units='MHz')
relax> relax_disp.r2eff_read(id='nu_14987', file='nu_14987_600MHz.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
disp_frq=14987, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=None, data_col=4,
error_col=5, sep=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_14987_600MHz.list'
for reading.
# mol_name res_num res_name spin_num spin_name R2eff
R2eff_error
None 54 Trp None None
6.51750797278 0.833397658203
None 52 Trp None None
9.67507931703 0.983193066509
None 27 Trp None None
3.08636451247 0.674090065044
None 23 Trp None None
3.19795453107 0.416749283078
None 51 Trp None None
6.77003530459 0.69567554334
None 55 Trp None None
4.64196677816 0.599331854064
The spectrum ID 'nu_14987' spin-lock field strength is set to 14.987 kHz.
relax> relax_data.read(ri_id='600MHz', ri_type='R1', frq=600200000.0,
file='R1.out',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/R1.out'
for reading.
The following 600.2 MHz R1 relaxation data with the ID '600MHz' has been
loaded into the relax data store:
# Spin_ID Value Error
:55@N 0.036 0.01
:54@N 0.068 0.005
:27@N 0.027 0.007
:23@N 0.03 0.002
:52@N 0.103 0.006
:51@N 0.077 0.005
relax> chemical_shift.read(file='nu_2000_ncyc1.list',
dir='/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax',
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, sep=None, spin_id=None)
Opening the file
'/data/people/pma/software/relax-3.2.1/PX_data/R2eff_Ubi_MPD_relax/nu_2000_ncyc1.list'
for reading.
Sparky formatted data file.
Number of header lines found: 1
2D peak list detected.
RelaxWarning: Cannot find the spin :55@HN within the sequence.
RelaxWarning: Cannot find the spin :54@HN within the sequence.
RelaxWarning: Cannot find the spin :27@HN within the sequence.
RelaxWarning: Cannot find the spin :23@HN within the sequence.
RelaxWarning: Cannot find the spin :52@HN within the sequence.
RelaxWarning: Cannot find the spin :51@HN within the sequence.
The following chemical shifts have been loaded into the relax data store:
# Spin_ID Chemical shift
:55@N 108.93755
:54@N 118.52423
:27@N 117.04146
:23@N 119.5115
:52@N 120.66282
:51@N 123.45963
=======================================
= Relaxation dispersion auto-analysis =
=======================================
Variable checking
=================
The dispersion auto-analysis variables are OK.
--------------------
- The 'MP05' model -
--------------------
relax> pipe.copy(pipe_from='base pipe', pipe_to='MP05 - relax_disp',
bundle_to='relax_disp')
relax> pipe.switch(pipe_name='MP05 - relax_disp')
relax> relax_disp.select_model(model='MP05')
The Miloushev and Palmer (2005) off-resonance 2-site model for R1rho-type
experiments.
Optimisation
============
relax> relax_disp.insignificance(level=1.0)
Deselecting spin ':23@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':27@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':51@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':52@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':54@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':55@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Nesting and model equivalence checks
------------------------------------
No model nesting or model equivalence detected.
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
relax> minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000,
constraints=True, scaling=True, verbosity=1)
relax> eliminate(function=None, args=None)
Results writing
===============
relax> relax_disp.plot_disp_curves(dir='./test_R1rho_R2eff//MP05',
num_points=1000, extend=500.0, force=True)
Opening the file './test_R1rho_R2eff//MP05/grace2images.py' for writing.
relax> relax_disp.write_disp_curves(dir='./test_R1rho_R2eff//MP05',
force=True)
relax> value.write(param='theta', file='theta.out',
dir='./test_R1rho_R2eff//MP05', scaling=1.0, comment=None, bc=False,
force=True)
Opening the file './test_R1rho_R2eff//MP05/theta.out' for writing.
relax> value.write(param='w_eff', file='w_eff.out',
dir='./test_R1rho_R2eff//MP05', scaling=1.0, comment=None, bc=False,
force=True)
Opening the file './test_R1rho_R2eff//MP05/w_eff.out' for writing.
relax> value.write(param='r2', file='r1rho0.out',
dir='./test_R1rho_R2eff//MP05', scaling=1.0, comment=None, bc=False,
force=True)
Opening the file './test_R1rho_R2eff//MP05/r1rho0.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='r2', spin_id=None,
plot_data='value', file='r1rho0.agr', dir='./test_R1rho_R2eff//MP05',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//MP05/r1rho0.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> value.write(param='pA', file='pA.out', dir='./test_R1rho_R2eff//MP05',
scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//MP05/pA.out' for writing.
relax> value.write(param='pB', file='pB.out', dir='./test_R1rho_R2eff//MP05',
scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//MP05/pB.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='pA', spin_id=None,
plot_data='value', file='pA.agr', dir='./test_R1rho_R2eff//MP05', force=True,
norm=False)
Opening the file './test_R1rho_R2eff//MP05/pA.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='res_num', y_data_type='pB', spin_id=None,
plot_data='value', file='pB.agr', dir='./test_R1rho_R2eff//MP05', force=True,
norm=False)
Opening the file './test_R1rho_R2eff//MP05/pB.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> value.write(param='dw', file='dw.out', dir='./test_R1rho_R2eff//MP05',
scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//MP05/dw.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='dw', spin_id=None,
plot_data='value', file='dw.agr', dir='./test_R1rho_R2eff//MP05', force=True,
norm=False)
Opening the file './test_R1rho_R2eff//MP05/dw.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> value.write(param='k_AB', file='k_AB.out',
dir='./test_R1rho_R2eff//MP05', scaling=1.0, comment=None, bc=False,
force=True)
Opening the file './test_R1rho_R2eff//MP05/k_AB.out' for writing.
relax> value.write(param='kex', file='kex.out',
dir='./test_R1rho_R2eff//MP05', scaling=1.0, comment=None, bc=False,
force=True)
Opening the file './test_R1rho_R2eff//MP05/kex.out' for writing.
relax> value.write(param='tex', file='tex.out',
dir='./test_R1rho_R2eff//MP05', scaling=1.0, comment=None, bc=False,
force=True)
Opening the file './test_R1rho_R2eff//MP05/tex.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='k_AB', spin_id=None,
plot_data='value', file='k_AB.agr', dir='./test_R1rho_R2eff//MP05',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//MP05/k_AB.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='res_num', y_data_type='kex', spin_id=None,
plot_data='value', file='kex.agr', dir='./test_R1rho_R2eff//MP05',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//MP05/kex.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='res_num', y_data_type='tex', spin_id=None,
plot_data='value', file='tex.agr', dir='./test_R1rho_R2eff//MP05',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//MP05/tex.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> value.write(param='chi2', file='chi2.out',
dir='./test_R1rho_R2eff//MP05', scaling=1.0, comment=None, bc=False,
force=True)
Opening the file './test_R1rho_R2eff//MP05/chi2.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='chi2', spin_id=None,
plot_data='value', file='chi2.agr', dir='./test_R1rho_R2eff//MP05',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//MP05/chi2.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> results.write(file='results', dir='./test_R1rho_R2eff//MP05',
compress_type=1, force=True)
Opening the file './test_R1rho_R2eff//MP05/results.bz2' for writing.
-------------------------------
- The 'NS R1rho 2-site' model -
-------------------------------
relax> pipe.copy(pipe_from='base pipe', pipe_to='NS R1rho 2-site -
relax_disp', bundle_to='relax_disp')
relax> pipe.switch(pipe_name='NS R1rho 2-site - relax_disp')
relax> relax_disp.select_model(model='NS R1rho 2-site')
The reduced numerical solution for the 2-site Bloch-McConnell equations using
3D magnetisation vectors for R1rho-type experiments, whereby the
simplification R20A = R20B is assumed.
Optimisation
============
relax> relax_disp.insignificance(level=1.0)
Deselecting spin ':23@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':27@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':51@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':52@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':54@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ':55@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Nesting and model equivalence checks
------------------------------------
Model equivalence detected, copying the optimised parameters from the
analytic 'MP05 - relax_disp' model rather than performing a grid search.
relax> minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000,
constraints=True, scaling=True, verbosity=1)
relax> eliminate(function=None, args=None)
Results writing
===============
relax> relax_disp.plot_disp_curves(dir='./test_R1rho_R2eff//NS R1rho 2-site',
num_points=1000, extend=500.0, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/grace2images.py' for
writing.
relax> relax_disp.write_disp_curves(dir='./test_R1rho_R2eff//NS R1rho
2-site', force=True)
relax> value.write(param='theta', file='theta.out',
dir='./test_R1rho_R2eff//NS R1rho 2-site', scaling=1.0, comment=None,
bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/theta.out' for writing.
relax> value.write(param='w_eff', file='w_eff.out',
dir='./test_R1rho_R2eff//NS R1rho 2-site', scaling=1.0, comment=None,
bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/w_eff.out' for writing.
relax> value.write(param='r2', file='r1rho0.out', dir='./test_R1rho_R2eff//NS
R1rho 2-site', scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/r1rho0.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='r2', spin_id=None,
plot_data='value', file='r1rho0.agr', dir='./test_R1rho_R2eff//NS R1rho
2-site', force=True, norm=False)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/r1rho0.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> value.write(param='pA', file='pA.out', dir='./test_R1rho_R2eff//NS
R1rho 2-site', scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/pA.out' for writing.
relax> value.write(param='pB', file='pB.out', dir='./test_R1rho_R2eff//NS
R1rho 2-site', scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/pB.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='pA', spin_id=None,
plot_data='value', file='pA.agr', dir='./test_R1rho_R2eff//NS R1rho 2-site',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/pA.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='res_num', y_data_type='pB', spin_id=None,
plot_data='value', file='pB.agr', dir='./test_R1rho_R2eff//NS R1rho 2-site',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/pB.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> value.write(param='dw', file='dw.out', dir='./test_R1rho_R2eff//NS
R1rho 2-site', scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/dw.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='dw', spin_id=None,
plot_data='value', file='dw.agr', dir='./test_R1rho_R2eff//NS R1rho 2-site',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/dw.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> value.write(param='k_AB', file='k_AB.out', dir='./test_R1rho_R2eff//NS
R1rho 2-site', scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/k_AB.out' for writing.
relax> value.write(param='kex', file='kex.out', dir='./test_R1rho_R2eff//NS
R1rho 2-site', scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/kex.out' for writing.
relax> value.write(param='tex', file='tex.out', dir='./test_R1rho_R2eff//NS
R1rho 2-site', scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/tex.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='k_AB', spin_id=None,
plot_data='value', file='k_AB.agr', dir='./test_R1rho_R2eff//NS R1rho
2-site', force=True, norm=False)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/k_AB.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='res_num', y_data_type='kex', spin_id=None,
plot_data='value', file='kex.agr', dir='./test_R1rho_R2eff//NS R1rho 2-site',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/kex.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='res_num', y_data_type='tex', spin_id=None,
plot_data='value', file='tex.agr', dir='./test_R1rho_R2eff//NS R1rho 2-site',
force=True, norm=False)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/tex.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> value.write(param='chi2', file='chi2.out', dir='./test_R1rho_R2eff//NS
R1rho 2-site', scaling=1.0, comment=None, bc=False, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/chi2.out' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='chi2', spin_id=None,
plot_data='value', file='chi2.agr', dir='./test_R1rho_R2eff//NS R1rho
2-site', force=True, norm=False)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/chi2.agr' for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> results.write(file='results', dir='./test_R1rho_R2eff//NS R1rho
2-site', compress_type=1, force=True)
Opening the file './test_R1rho_R2eff//NS R1rho 2-site/results.bz2' for
writing.
Final results
=============
relax> model_selection(method='AIC', modsel_pipe='final - relax_disp',
bundle='relax_disp', pipes=['MP05 - relax_disp', 'NS R1rho 2-site -
relax_disp'])
AIC model selection.
The spin cluster [':23@N'].
No model has been selected.
The spin cluster [':27@N'].
No model has been selected.
The spin cluster [':51@N'].
No model has been selected.
The spin cluster [':52@N'].
No model has been selected.
The spin cluster [':54@N'].
No model has been selected.
The spin cluster [':55@N'].
No model has been selected.
RelaxError: The data pipe 'final - relax_disp' has not been created yet.
Re: R1rho RD analysis