I think I have it working now. I resolved it by uncommenting the spectrum.baseplane_rmsd line and removing the spin_id part of that command. I knew it was something simple to do with using the new script compared to the old one. Thanks for your help.
On Wed, Mar 9, 2011 at 11:12 AM, Edward d'Auvergne <[email protected]> wrote: > Hi, > > relax will run fine without these peaks included. I have modified > relax to print out more meaningful warnings when unassigned NMRView > peaks are encountered. The problem looks like there is another issue. > Would you be able to attach all the NMRView peak lists? But please > delete all but the first two assignment lines in each. Do you see an > error message? Could you run your analysis again, but on the > truncated NMRView files? Does it work if you uncomment the baseplane > RMSD user function? > > Regards, > > Edward > > > On 9 March 2011 16:59, Elio Cino <[email protected]> wrote: >> I realize that those peaks are not labelled. They were unassigned >> residues. In the previous version I used 1.3.3 I had many unlabeled >> peaks and there was not any problem running relax. Do I need to remove >> these lines from the xpk in order to get relax working now? My problem >> is that relax seems to abort and I do not get any of the relaxation >> data output, just blank files. >> >> On Wed, Mar 9, 2011 at 5:53 AM, Edward d'Auvergne <[email protected]> >> wrote: >>> Hi, >>> >>> Unfortunately this print out information is not enough for me to >>> determine what the problem is. The problem could be earlier when you >>> read in the sequence. If you could submit a bug report, that would be >>> much appreciated (https://gna.org/bugs/?func=additem&group=relax). If >>> you could include the full print out from relax, the information you >>> get from typing 'relax --info', your script, the sequence file, and >>> the 500.xpk file, it would be much appreciated and I should be able to >>> then fix the problem in a few minutes. If you would like to keep the >>> data confidential, you could remove all but the first 2 peaks from the >>> 500.xpk file (and the sequence file), and even randomise the value of >>> the peak height. Essentially if I have a tiny randomised data set and >>> relax script which demonstrates the bug, I would add this to the relax >>> test suite. That will allow me to debug it in a few minutes and also >>> to ensure that this data will be readable for the lifetime of relax. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 8 March 2011 21:59, Elio Cino <[email protected]> wrote: >>>> Hello. I have not used relax in a while and upgraded to the latest >>>> 1.3.10 before doing my curve fitting. I am having a problem with the >>>> sample script and have pasted a bit out the output below. I am not >>>> sure what is going on here. Any help is appreciated. Thanks. >>>> >>>> Opening the file '500.xpk' for reading. >>>> NMRView formatted data file. >>>> >>>> Number of header lines: 6 >>>> Using peak heights. >>>> RelaxWarning: Cannot find the spin :@ within the sequence. >>>> RelaxWarning: Cannot find the spin :@ within the sequence. >>>> RelaxWarning: Cannot find the spin :@ within the sequence. >>>> >>>> >>>> -- >>>> Elio Cino >>>> >>>> _______________________________________________ >>>> relax (http://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 >>>> >>> >> >> >> >> -- >> Elio Cino >> > -- Elio Cino _______________________________________________ relax (http://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
