Re: relax_fit problem -- March 09, 2011 - 17:45

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 <edward@xxxxxxxxxxxxx> 
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 <herfworm@xxxxxxxxx> 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 <edward@xxxxxxxxxxxxx> 
> > 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 <herfworm@xxxxxxxxx> 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)
> > > >
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> >
> >
> > --
> > Elio Cino



-- 
Elio Cino