Cheers! The column numbering has changed - the reason was that many users were confused with the concept of counting starting at zero. There was also a default of the residue number and name columns being set to the first and second columns as well - this was removed for the organic chemists who do not have residues, as having default residue columns caused failures for organic molecules. So I'm guessing the script you sent to Nick only had the spin name column set to 2 and the res_num_col and res_name_col arguments not set. That would make sense and would explain the output Nick sees. Specifying the columns for this user function should fix this problem, though there might be some relax version differences later on in the script which will cause more problems. The user function documentation should be able to explain and resolve these issues as well.
Regards, Edward On 6 September 2012 21:17, Madeleine Strickland <[email protected]> wrote: > Hi Nicholas, this data is from a couple of years ago run on red hat > enterprise. The issue here is that column definitions are different, in your > version column 0 doesn't exist. You need to change the sequence line to > this.... > > sequnce.read('sequence.out', res_num_col=1, res_name_col=2, spin_name_col=3) > > I used relax 1.3.9 for this, or earlier, which is why definitions are > slightly different. > > Hope this helps. > > Maddy > > Not sure about the monte carlo errors though! > > [email protected] wrote: >> >> Send relax-users mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.gna.org/listinfo/relax-users >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of relax-users digest..." >> >> >> Today's Topics: >> >> 1. Re: About model-free analysis (Edward d'Auvergne) >> 2. Error message and test failures from the relax test suites >> (Nicolas Doucet) >> >> >> ________________________________ >> >> >> Message: 1 >> Date: Thu, 6 Sep 2012 14:14:19 +0200 >> From: "Edward d'Auvergne" <[email protected]> >> To: [email protected] >> Cc: [email protected] >> Subject: Re: About model-free analysis >> Message-ID: >> <caed9py_r8s31my1w19uh5ss7cjhh6wjles62suuhsf8sxee...@mail.gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Hi Mengjun, >> >> I've been looking for the relevant links as we have discussed this >> topic a number of times on the relax-users mailing list. One good >> reference would be to read all the messages sent by myself, Sebastien >> Morin, Alex Hansen, Michael Marlow, and Gary Thompson in the thread >> called "CSA & bond length" starting at: >> >> http://thread.gmane.org/gmane.science.nmr.relax.user/192 >> >> and continued on the relax-devel mailing list at: >> >> http://thread.gmane.org/gmane.science.nmr.relax.devel/1115 >> http://thread.gmane.org/gmane.science.nmr.relax.devel/1116 >> http://thread.gmane.org/gmane.science.nmr.relax.devel/1119 >> >> I'll keep looking for the other threads which discuss this, as this >> was recently talked about, but I cannot find the messages right now. >> In summary, for protein backbone NH data you should really use 1.02 >> Angstrom with -172 ppm CSA. The value of -160 ppm is from solid state >> studies of peptides and is an underestimation for solution NMR. >> >> There is CSA variability but the amount of variability is highly >> debated. Some of Nico Tjandra's estimates of variability might be on >> the high side, David Fushman's might be more reasonable. In reality, >> no one really knows what the real CSA and bond length values are and >> no one has reliably de-convoluted the internal ps-ns dynamics from >> these parameters to be able to properly answer this question. >> Therefore everyone takes the compromise of 1.02 A with roughly -172 >> ppm (the Hall and Fushman average value). There is another school of >> thought from the NIH direction of Washington DC which says we should >> use 1.04 A with -160 ppm. However this will generally shift the order >> parameters higher and closer to one - causing the optimisation >> algorithms to have severe problems and failures due to the convolution >> of the optimisation space that this results in So it is not >> recommended for a model-free analysis - the removal of zero-point >> motions concept. As long as you are consistent and know that the >> order parameters are a relative concept rather than absolute - then >> you can compare different states. I hope this helps. >> >> Regards, >> >> Edward >> >> >> P. S. If you do solve this problem reliably, you will probably >> receive quite a few citations and make a name for yourself. However >> the NMR field has being trying to solve this unsuccessfully for the >> last who knows how many decades. So I wouldn't recommend trying >> unless you have an incredible amount of spare time and don't mind >> diving into the deepest depths of NMR and physics theory. >> >> >> >> >> On 5 September 2012 18:09, <[email protected]> wrote: >> > Hi, >> > >> > When doing model-free analysis, NH bond length set to 1.02 angstrom >> > normally, but it is a little bit different for different amino acid >> > residue; >> > and >> > also the N chemical shift anisotropy set to say -160 ppm normally, but >> > CSA >> > is changing from residue to residue, How do Relax solve such kind of >> > problem when doing model-free analysis? >> > >> > Regards, >> > >> > Mengjun Xue >> > >> > >> > >> > >> > >> > >> ________________________________ >> >> > 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 >> >> >> >> ________________________________ >> >> >> Message: 2 >> Date: Thu, 6 Sep 2012 14:44:32 -0400 >> From: Nicolas Doucet <[email protected]> >> To: Maddy Strickland <[email protected]> >> Cc: "[email protected]" <[email protected]>, Edward d'Auvergne >> <[email protected]> >> Subject: Error message and test failures from the relax test suites >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset="iso-8859-1" >> >> 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 >> > >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: </public/relax-users/attachments/20120906/87d081be/attachment.html> >> >> ________________________________ >> >> >> ________________________________ >> >> 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 >> >> End of relax-users Digest, Vol 74, Issue 8 >> ****************************************** > > > _______________________________________________ > 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
