Error message and test failures from the relax test suites -- September 06, 2012

Maddy,

Thanks a lot for your files. After deleting the output files, we tried to run your T1 'as is' to no avail. As you can see from the message below, we get an error very similar to the one we previously saw with our own files. It cannot find spins within the sequence. Can you really run the files you sent us without a single issue?

I'm starting to wonder whether our problem isn't related to software or module installation. Are you running relax on linux? We're running everything on Ubuntu 12.04 LTS with Python 2.7.3. We tried on 32-bit and 64-bit machines. No difference. I did install Python, NumPy, SciPy and wxPython as dependencies and the GUI also works fine when I boot it up. Perhaps I'm missing something.

Anyway, I also ran the relax test suites and I'm getting the following Monte Carlo failures:

System/functional tests:

FAIL: test_monte_carlo_sims (test_suite.system_tests.n_state_model.N_state_model)

Test the Monte Carlo simulation data of fitting RDCs and PCSs.

GUI tests:

FAIL: test_monte_carlo_sims (test_suite.gui_tests.n_state_model.N_state_model)
Test the Monte Carlo simulation data of fitting RDCs and PCSs.

The 'unit test' is fine. However, the error message we're getting here is clearly unrelated to any type of calculation. The software simply doesn't recognize spins, which could make sense considering they're not written the same way in your sequence.out and list files.

I'm a bit puzzled as to why it works for you and not for us.

Nick

Nicolas Doucet

Assistant Professor

INRS - Institut Armand-Frappier

University of Quebec

Institut Pasteur International Network

531 Boulevard des Prairies

Laval (Quebec) H7V 1B7 CANADA

Phone: (450) 687-5010 #4212

Fax: (450) 686-5501

Email: nicolas.doucet@xxxxxxxxxxx

Web: http://www.profs.inrs.ca/ndoucet/

Begin forwarded message:

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.

script = 'T1_curve_fit.py'
----------------------------------------------------------------------------------------------------

###############################################################################
# #
# 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 sequence and spins
sequence.read('sequence.out', spin_name_col=2)

# Spectrum names.
names = [
'T1_0111',
'T1_0333',

'T1_0555',
'T1_111',
'T1_1998',
'T1_333',
'T1_4995',
'T1_666',
'T1_888',

]

# Relaxation times (in seconds).
times = [
0.0111,
0.0333,
0.0555,
0.111,
0.1998,
0.333,
0.4995,
0.666,
0.888,
]

# Loop over the spectra.
for i in xrange(len(names)):
# Load the peak intensities.
spectrum.read_intensities(file=names[i]+'.list', spectrum_id=names[i], int_method='height')

# Set the relaxation times.
relax_fit.relax_time(time=times[i], spectrum_id=names[i])

# Set the baseplane error
spectrum.baseplane_rmsd(error=461070, spectrum_id='T1_0111')

spectrum.baseplane_rmsd(error=437800, spectrum_id='T1_0333')
spectrum.baseplane_rmsd(error=440440, spectrum_id='T1_0555')
spectrum.baseplane_rmsd(error=426960, spectrum_id='T1_111')

spectrum.baseplane_rmsd(error=376040, spectrum_id='T1_1998')
spectrum.baseplane_rmsd(error=323600, spectrum_id='T1_333')
spectrum.baseplane_rmsd(error=262310, spectrum_id='T1_4995')

spectrum.baseplane_rmsd(error=212290, spectrum_id='T1_666')
spectrum.baseplane_rmsd(error=164550, spectrum_id='T1_888')

# 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=500)
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='rx', file='rx.agr', force=True) # Relaxation rate.

# Display the Grace plots.
grace.view(file='rx.agr')

# Save the program state.
state.save('rx.save', force=True)
----------------------------------------------------------------------------------------------------

relax> pipe.create(pipe_name='rx', pipe_type='relax_fit', bundle=None)

relax> sequence.read(file='sequence.out', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=2, sep=None, spin_id=None)

Opening the file 'sequence.out' for reading.
# mol_name res_num res_name spin_num spin_name
None None None None Res_name
None None None None Trp

None None None None Trp
None None None None Ser
None None None None Asn
None None None None Ser
None None None None Ser
None None None None Ala
None None None None Thr

None None None None Pro
None None None None Ile
None None None None Val
None None None None Gln
None None None None Phe
None None None None Gln
None None None None Gly

None None None None Glu
None None None None Ser
None None None None Asn
None None None None Cys
None None None None Leu
None None None None Lys
None None None None Cys

None None None None Phe
None None None None Arg
None None None None Tyr
None None None None Arg
None None None None Leu
None None None None Asn
None None None None Asp

None None None None Lys
None None None None His
None None None None Arg
None None None None His
None None None None Leu
None None None None Phe
None None None None Asp

None None None None Leu
None None None None Ile
None None None None Ser
None None None None Ser
None None None None Thr
None None None None Trp
None None None None His

None None None None Trp
None None None None Ala
None None None None Ser
None None None None Pro
None None None None Lys
None None None None Ala
None None None None Pro

None None None None His
None None None None Lys
None None None None His
None None None None Ala
None None None None Ile
None None None None Val
None None None None Thr

None None None None Val
None None None None Thr
None None None None Tyr
None None None None His
None None None None Ser
None None None None Glu
None None None None Glu

None None None None Gln
None None None None Arg
None None None None Gln
None None None None Gln
None None None None Phe
None None None None Leu
None None None None Asn

None None None None Val
None None None None Val
None None None None Lys
None None None None Ile
None None None None Pro
None None None None Pro
None None None None Thr

None None None None Ile
None None None None Arg
None None None None His
None None None None Ala
None None None None Leu
None None None None Gly
None None None None Phe

None None None None Met
None None None None Ser
None None None None Met
None None None None His
None None None None Leu
None None None None Leu

relax> spectrum.read_intensities(file='T1_0111.list', dir=None, spectrum_id='T1_0111', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)

Opening the file 'T1_0111.list' for reading.
Sparky formatted data file.

Number of header lines found: 1
RelaxWarning: Cannot find the spin :42@N within the sequence.

RelaxWarning: Cannot find the spin :79@N within the sequence.
RelaxWarning: Cannot find the spin :35@N within the sequence.
RelaxWarning: Cannot find the spin :39@N within the sequence.
RelaxWarning: Cannot find the spin :80@N within the sequence.
RelaxWarning: Cannot find the spin :37@N within the sequence.
RelaxWarning: Cannot find the spin :49@N within the sequence.
RelaxWarning: Cannot find the spin :20@N within the sequence.

RelaxWarning: Cannot find the spin :26@N within the sequence.
RelaxWarning: Cannot find the spin :66@N within the sequence.
RelaxWarning: Cannot find the spin :30@N within the sequence.
RelaxWarning: Cannot find the spin :74@N within the sequence.
RelaxWarning: Cannot find the spin :36@N within the sequence.
RelaxWarning: Cannot find the spin :83@N within the sequence.
RelaxWarning: Cannot find the spin :29@N within the sequence.

RelaxWarning: Cannot find the spin :7@N within the sequence.
RelaxWarning: Cannot find the spin :31@N within the sequence.
RelaxWarning: Cannot find the spin :59@N within the sequence.
RelaxWarning: Cannot find the spin :71@N within the sequence.

RelaxWarning: Cannot find the spin :13@N within the sequence.
RelaxWarning: Cannot find the spin :75@N within the sequence.
RelaxWarning: Cannot find the spin :22@N within the sequence.
RelaxWarning: Cannot find the spin :68@N within the sequence.
RelaxWarning: Cannot find the spin :41@N within the sequence.
RelaxWarning: Cannot find the spin :67@N within the sequence.
RelaxWarning: Cannot find the spin :52@N within the sequence.

RelaxWarning: Cannot find the spin :4@N within the sequence.
RelaxWarning: Cannot find the spin :86@N within the sequence.
RelaxWarning: Cannot find the spin :10@N within the sequence.
RelaxWarning: Cannot find the spin :54@N within the sequence.

RelaxWarning: Cannot find the spin :88@N within the sequence.
RelaxWarning: Cannot find the spin :34@N within the sequence.
RelaxWarning: Cannot find the spin :60@N within the sequence.
RelaxWarning: Cannot find the spin :65@N within the sequence.
RelaxWarning: Cannot find the spin :57@N within the sequence.
RelaxWarning: Cannot find the spin :15@N within the sequence.
RelaxWarning: Cannot find the spin :78@N within the sequence.

RelaxWarning: Cannot find the spin :84@N within the sequence.
RelaxWarning: Cannot find the spin :25@N within the sequence.
RelaxWarning: Cannot find the spin :40@N within the sequence.
RelaxWarning: Cannot find the spin :56@N within the sequence.
RelaxWarning: Cannot find the spin :48@N within the sequence.
RelaxWarning: Cannot find the spin :61@N within the sequence.
RelaxWarning: Cannot find the spin :12@N within the sequence.

RelaxWarning: Cannot find the spin :53@N within the sequence.
RelaxWarning: Cannot find the spin :6@N within the sequence.
RelaxWarning: Cannot find the spin :43@N within the sequence.
RelaxWarning: Cannot find the spin :33@N within the sequence.

RelaxWarning: Cannot find the spin :72@N within the sequence.
RelaxWarning: Cannot find the spin :32@N within the sequence.
RelaxWarning: Cannot find the spin :16@N within the sequence.
RelaxWarning: Cannot find the spin :19@N within the sequence.
RelaxWarning: Cannot find the spin :11@N within the sequence.
RelaxWarning: Cannot find the spin :21@N within the sequence.
RelaxWarning: Cannot find the spin :58@N within the sequence.

RelaxWarning: Cannot find the spin :8@N within the sequence.
RelaxWarning: Cannot find the spin :28@N within the sequence.
RelaxWarning: Cannot find the spin :62@N within the sequence.
RelaxWarning: Cannot find the spin :45@N within the sequence.

RelaxWarning: Cannot find the spin :91@N within the sequence.
RelaxError: No data could be loaded from the peak list

Error message and test failures from the relax test suites

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