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> _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?18789> _______________________________________________ Message sent via/by Gna! http://gna.org/