Hi Nick, There are two issues you are seeing here. You are right about the test suite, this is unrelated. I'm not sure what the problem would be there, that would require more of the output. Would you be able to create a bug report for your test-suite issue at https://gna.org/bugs/?func=additem&group=relax ? That would be much appreciated. If you run relax with:
$ relax --test-suite > log 2> err The files 'log' and 'err' will contain much more information and can be attached to the bug report. Thanks! Such a report will allow the relax developers to track down the issue and fix it quickly for the next relax version. The second problem seems not to be with Maddy's data, but how you are trying to read it in. Unfortunately I don't know exactly how these files look like, but I can guess from the messages that the problem is in the script trying to read the data in. This starts with your user function call: 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) What really worries me here is that the residue number and name columns are not specified. I'm guessing that the format is that specified by Maddy in her message (http://thread.gmane.org/gmane.science.nmr.relax.user/1270): Res_num Res_name Spin_name 1 Trp N 2 Trp N Therefore you need to set the residue number column to 1, the residue name column to 2, and the spin name column to 3. Otherwise the sequence.read user function will not know what to do. With the user function being told that the spin name is in column 2, relax has created a set of spins (or atoms) with the residue name used for the spin (or atom) names - and as no molecule or residue has been specified, all these spins are located within a single unnamed and unnumbered residue! You can see this in the print out. All the spins you have loaded have the molecule name set to None, the residue name and number set to None, and the spin number set to None. The spin name column in the print out contains the residue names instead of the spin names. The next user function spectrum.read_intensities fails with messages such as: RelaxWarning: Cannot find the spin :42@N within the sequence. This is because relax is trying to locate the residue number 42 with the spin name 'N' which is the first line in the peak list. But there has been no such spin created because of the bad arguments to the sequence.read user function above, hence relax gives a warning saying that it cannot find the spin for that data. I have recently made relax throw a script terminating RelaxError from the spectrum.read_intensities user function, which is the last message you see. My intent here is to stop you going too far and not recognising that a fatal failure has occurred earlier in the script. I would suggest that for each user function call in your script, that you should very carefully read the documentation for that user function (either in the user manual PDF file which came with relax, online at http://www.nmr-relax.com/manual/Alphabetical_listing_user_functions.html, or in the prompt mode by typing "help(sequence.read)"). Specifying the correct arguments is extremely important, otherwise relax is unable to interpret what you would like performed and it will naturally fail. Hopefully this will allow the script and relax to run successfully. Regards, Edward On 6 September 2012 20:44, Nicolas Doucet <[email protected]> wrote: > 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: [email protected] > 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 > > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-users mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-users > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
