Hi Paolo, Welcome to the relax mailing lists. I've looked at your suggestion, and it might work. Unfortunately I wrote this mfout parsing code a long, long time ago, and it is not very flexible. There is now the pystarlib project (http://code.google.com/p/pystarlib/) which would be a much better way of processing these STAR formatted mfout files. This is included with the bmrblib project (http://gna.org/projects/bmrblib/) which will be bundled with relax in the future. However, considering that Art Palmer has stopped development of his program Modelfree for over a decade (it's been in maintenance mode since 04/15/98), this solution would probably be too much effort.
As Seb said, would you be able to share some of your data? If you could attach an mfout file with and without simulations to the bug report (http://gna.org/bugs/?18391), that would be much appreciated. This only needs to have data for 1 or 2 spins (in the mfdata, etc files), and this truncated data can be randomised if total secrecy is needed. I would then be able to add both files to the relax test suite and add checks to see if relax can read the files and data correctly. This will guarantee that relax will be able to read these mfout file for eternity. Another advantage of adding this to the test suite will be that I can compare the reading of different mfout files. I have an old file from 2002 generated by Modelfree 4.15 which relax 1.3 can read perfectly as the code currently is. Which version of Modelfree have you used? Maybe this is a version difference. Cheers, Edward P. S. If you insist on using Modelfree4, I would recommend a few source code changes so that you obtain much better results. Firstly you need to massively increase the precision by the following change: diff -r modelfree/fglob.F modelfree_orig/fglob.F 49c49 < parameter (maxit=10000000,convrg=1E-25) --- > parameter (maxit=50,convrg=0.0001) These numbers are much more reasonable and match the default precision of relax. This low precision was because this code was originally written to work on this http://en.wikipedia.org/wiki/VAX, without taking a lifetime to complete. The high precision calculations are no longer a problem for modern machines. On 22 July 2011 12:18, Sébastien Morin <[email protected]> wrote: > Dear Paolo, > > First of all, welcome to relax. > > Second, thanks for submitting this bug report as well as a solution. > > Have you tested the solution with data without MC simulations performed ? > > Could you share a part of your dataset (possibly randomized) such that we > can reproduce the bug and include the data into the test suite for the bug > never to come back again, please ? > > Thanks ! > > > Séb :) > > > On 11-07-21 2:42 PM, Paolo Calligari wrote: >> >> URL: >> <http://gna.org/bugs/?18391> >> >> Summary: Palmer extract. Error in chi2 read when 'sims' >> is >> different from 0 >> Project: relax >> Submitted by: pcalligari >> Submitted on: Thu 21 Jul 2011 12:42:45 PM GMT >> Category: relax's source code >> Severity: 3 - Normal >> Priority: 5 - Normal >> Status: None >> Privacy: Public >> Assigned to: None >> Originator Name: >> Originator Email: >> Open/Closed: Open >> Discussion Lock: Any >> Release: 1.3.10 >> Operating System: All systems >> >> _______________________________________________________ >> >> Details: >> >> When trying to read palmer's modelfree output performed with MC >> simulations, >> the module palmer.extract(dir) fails. >> >> Looking to the code, I'd say that line 731 in generic_fns/palmer.py >> should be changed from >> >> row = split(mfout_lines[chi2_pos + 2 + 22*pos]) >> >> to >> >> row = split(mfout_lines[chi2_pos + 2 + 41*pos]) >> >> >> I've tried this change and now it works fine. >> >> cheers, >> Paolo >> >> >> >> >> >> _______________________________________________________ >> >> Reply to this item at: >> >> <http://gna.org/bugs/?18391> >> >> _______________________________________________ >> Message sent via/by Gna! >> http://gna.org/ >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-devel 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-devel > > -- > Sébastien Morin, Ph.D. > Postdoctoral Fellow, S. Grzesiek NMR Laboratory > Department of Structural Biology > Biozentrum, Universität Basel > Klingelbergstrasse 70 > 4056 Basel > Switzerland > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-devel 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-devel > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel 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-devel
