Dear Dr. Edward d'Auvergne,
Thank you very much for answers. I have read the manual of relax and
checked the mf_multimodel.py.
I have changed the mf_multimodel.py into a new version according to my
data, and have tried to run it in scripts mode in Relax.
I started relax script mode by clicking the relax.py, and type
mf_multimodel, but Relax did not perform calculations, and a error
window came up:
mf_multimodel.py
Traceback (most recent call last):
File "<input>", line 1, in <module>
NameError: name 'mf_multimodel' is not defined
Attached please find the new mf_multimodel.py
I do not know how to start the calcultioin by mf_multimodel so that
the part of model free analysis can be performed. Perhaps something is
wrong in the new mf_multimodel.py.
Also I I have submitted it as a bug report.
Thank you very much.
With best regards,
Mengjun Xue
Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi Mengjun,
For your bug report at https://gna.org/bugs/?20173, I have changed the
title. It would be better if you chose a title which allows other
users looking at https://gna.org/bugs/index.php to instantly
understand what and where the bug is. In this case, the bug is simply
because the diffusion tensor has not been set up. I would suggest
looking at the sample script
sample_scripts/model_free/mf_multimodel.py to see how to perform part
of a model-free analysis in the GUI without using the auto-analyses
(note this is only a tiny part, please read the model-free chapter of
the user manual for the explanation why this is only 1/3 of one
iteration of up to 20 iterations).
I have eliminated the bug by having relax throw a RelaxError saying
that the diffusion tensor is not set up yet.
Cheers,
Edward
###############################################################################
#
#
# Copyright (C) 2003-2012 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/>.
#
#
#
###############################################################################
"""This script performs a model-free analysis for the models 'm0' to 'm9' (or
'tm0' to 'tm9')."""
# Set the data pipe names (also the names of preset model-free models).
#pipes = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8',
'tm9']
pipes = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
# Loop over the pipes.
for name in pipes:
# Create the data pipe.
pipe.create(name, 'mf')
# Set up the 15N spins.
sequence.read('noe.500.out', res_num_col=1)
spin.name('N')
spin.element(element='N', spin_id='@N')
spin.isotope('15N', spin_id='@N')
# Load a PDB file.
structure.read_pdb(file='C:\\Documents and Settings\\Mengjun
Xue\\Desktop\\Relax bugs\\Relax\\tutorial_pdc\\tutorial_pdc\\1UBQ_H.pdb',
dir=None, read_mol=None, set_mol_name=None, read_model=None,
set_model_num=None, parser='internal')
# Load the relaxation data.
bruker.read(ri_id='noe_600', file='C:\\Documents and Settings\\Mengjun
Xue\\Desktop\\Relax bugs\\Relax\\NOE demo.txt', dir=None)
bruker.read(ri_id='r1_600', file='C:\\Documents and Settings\\Mengjun
Xue\\Desktop\\Relax bugs\\Relax\\T1 demo.txt', dir=None)
bruker.read(ri_id='r2_600', file='C:\\Documents and Settings\\Mengjun
Xue\\Desktop\\Relax bugs\\Relax\\T2 demo.txt', dir=None) # Set up the
diffusion tensor.
diffusion_tensor.init(1e-8, fixed=True)
#diffusion_tensor.init((1e-8, 1.0, 60, 290), param_types=0,
spheroid_type='oblate', fixed=True)
# Generate the 1H spins for the magnetic dipole-dipole relaxation
interaction.
sequence.attach_protons()
# Define the magnetic dipole-dipole relaxation interaction.
dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
structure.get_pos('@N')
structure.get_pos('@H')
dipole_pair.unit_vectors()
# Define the chemical shift relaxation interaction.
value.set(-172 * 1e-6, 'csa', spin_id='@N')
# Select the model-free model.
model_free.select_model(model=name)
# Minimise.
grid_search(inc=11)
minimise('newton')
# Write the results.
results.write(file='results', force=True)
# Save the program state.
state.save('save', force=True)
Re: [bug #20173] bugs in Relax