Hi Elio,
Thanks for submitting a bug report. I tried to run the script, but
there was a slight problem. Could you attach the other data files to
the bug report as well? You only need the first 1 or 2 data lines,
i.e. the entire 500.xpk file should look like:
label dataset sw sf
1H 15N
hsqc_500.nv
4000.0 1822.97094727
599.619995117 60.7659988403
1H.L 1H.P 1H.W 1H.B 1H.E 1H.J 1H.U 15N.L 15N.P 15N.W 15N.B 15N.E 15N.J
15N.U vol int stat comment flag0
0 {13.HN} 9.48639 0.01764 0.02520 ++ {0.0} {} {13.N} 127.72855 0.22035
0.16922 ++ {0.0} {} 0.762715339661 0.2197 0 {} 0
1 {67.HN} 9.43386 0.01111 0.01588 ++ {0.0} {} {67.N} 127.65032 0.15565
0.08565 ++ {0.0} {} 0.72598695755 0.1875 0 {} 0
The file you attached included data for all residues. The aim is to
come up with the absolute minimum amount of data which still triggers
the bug. If you do only include the data for residues 13 (and maybe
67), could you check that the script and relax still produce the bug?
Cheers,
Edward
On 5 October 2011 17:07, anonymous <[email protected]> wrote:
>
> 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/
>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
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