URL:
<http://gna.org/bugs/?18789>
Summary: no error values using relax_fit.py with
non-duplicated spectra
Project: relax
Submitted by: None
Submitted on: Wed 05 Oct 2011 03:07:16 PM UTC
Category: None
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: 1.3.12
Operating System: None
_______________________________________________________
Details:
Hello. I typically use duplicated spectra, but this time I only have
non-duplicated data. From what I understand from the relax manual, residue
specific error values should still be attainable by setting the
spectrum.baseplane_rmsd for each spectrum id. However, I still get error
values of 0. Could anyone please point me in the right direction here? I
have pasted the scrip I am using below and also attached the scrip and one
of my xpk files for testing. Thanks very much.
###############################################################################
#
#
# 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 relaxation curve fitting.
######################################
# Create the 'rx' data pipe.
pipe.create('rx', 'relax_fit')
# Load the backbone amide 15N spins from a PDB file.
structure.read_pdb('1ubq.pdb')
structure.load_spins(spin_id='@N')
# Spectrum names.
names = [
'500',
'010',
'040',
'420',
'080',
'340',
'120',
'280',
'160',
'220'
]
# Relaxation times (in seconds).
times = [
0.500,
0.010,
0.040,
0.420,
0.080,
0.340,
0.120,
0.280,
0.160,
0.220
]
# Loop over the spectra.
for i in xrange(len(names)):
# Load the peak intensities.
spectrum.read_intensities(file=names[i]+'.xpk', spectrum_id=names[i],
int_method='height')
# Set the relaxation times.
relax_fit.relax_time(time=times[i], spectrum_id=names[i])
spectrum.baseplane_rmsd(error=26500, spectrum_id='500', spin_id=None)
spectrum.baseplane_rmsd(error=16700, spectrum_id='010', spin_id=None)
spectrum.baseplane_rmsd(error=18200, spectrum_id='040', spin_id=None)
spectrum.baseplane_rmsd(error=21100, spectrum_id='420', spin_id=None)
spectrum.baseplane_rmsd(error=12300, spectrum_id='080', spin_id=None)
spectrum.baseplane_rmsd(error=17800, spectrum_id='340', spin_id=None)
spectrum.baseplane_rmsd(error=12200, spectrum_id='120', spin_id=None)
spectrum.baseplane_rmsd(error=14500, spectrum_id='280', spin_id=None)
spectrum.baseplane_rmsd(error=11100, spectrum_id='160', spin_id=None)
spectrum.baseplane_rmsd(error=13400, spectrum_id='220', spin_id=None)
# Peak intensity error analysis.
spectrum.error_analysis()
# Deselect unresolved spins.
#deselect.read(file='unresolved')
# Set the relaxation curve type.
relax_fit.select_model('exp')
# Grid search.
grid_search(inc=11)
# Minimise.
minimise('simplex', scaling=False, constraints=False)
# Monte Carlo simulations.
monte_carlo.setup(number=5)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise('simplex', scaling=False, constraints=False)
monte_carlo.error_analysis()
# Save the relaxation rates.
value.write(param='rx', file='rx.out', force=True)
# Save the results.
results.write(file='results', force=True)
# Create Grace plots of the data.
grace.write(y_data_type='chi2', file='chi2.agr', force=True) # Minimised
chi-squared value.
grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial peak
intensity.
grace.write(y_data_type='rx', file='rx.agr', force=True) # Relaxation
rate.
grace.write(x_data_type='relax_times', y_data_type='int',
file='intensities.agr', force=True) # Average peak intensities.
grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='intensities_norm.agr', force=True) # Average peak intensities
(normalised).
# Display the Grace plots.
#grace.view(file='chi2.agr')
#grace.view(file='i0.agr')
#grace.view(file='rx.agr')
#grace.view(file='intensities.agr')
#grace.view(file='intensities_norm.agr')
# Save the program state.
state.save('rx.save', force=True)
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Wed 05 Oct 2011 03:07:16 PM UTC Name: relax_fit.py Size: 5kB By:
None
<http://gna.org/bugs/download.php?file_id=14201>
-------------------------------------------------------
Date: Wed 05 Oct 2011 03:07:16 PM UTC Name: 1ubq.pdb Size: 59kB By: None
<http://gna.org/bugs/download.php?file_id=14202>
-------------------------------------------------------
Date: Wed 05 Oct 2011 03:07:16 PM UTC Name: 500.xpk Size: 9kB By: None
<http://gna.org/bugs/download.php?file_id=14203>
_______________________________________________________
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<http://gna.org/bugs/?18789>
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Re: [bug #18789] no error values using relax_fit.py with non-duplicated spectra