URL:
<http://gna.org/bugs/?20174>
Summary: run mf_multimodel.py in relax
Project: relax
Submitted by: None
Submitted on: Mon 17 Sep 2012 04:30:17 PM UTC
Category: relax sample scripts
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email: mengjun.xue@xxxxxxxxxxxxxxxxxxxx
Open/Closed: Open
Discussion Lock: Any
Release: 2.1.0
Operating System: Microsoft Windows
_______________________________________________________
Details:
I started relax script mode by clicking the relax.py, and type
mf_multimodel,
but Relax did not continue to perform calculations, and a error window came
up:
relax 2.1.0
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2012 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.
mf_multimodel.py
Traceback (most recent call last):
File "<input>", line 1, in <module>
NameError: name 'mf_multimodel' is not defined
the text version of mf_multimodel.py is shown in following:
###############################################################################
#
#
# 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)
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Mon 17 Sep 2012 04:30:17 PM UTC Name: mf_multimodel.py Size: 4kB
By:
None
<http://gna.org/bugs/download.php?file_id=16587>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?20174>
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Re: [bug #20174] run mf_multimodel.py in relax