Hi,
This is an interesting situation, that looks like an old bug I
eliminated many years ago that has somehow returned. I'll definitely
have to fix this. Would you be able to create a bug report for this
issue? It would be useful to run relax with the '--debug' command
line flag to produce a more detailed RelaxError message and to
possibly attach the save file this produces (I think this now occurs
automatically with the debug flag in the 1.2 line) to the bug report.
If there is no save file, attaching the file
'local_tm/aic/results.bz2' would also be of value for debugging. Or
better still, if you add a command to save the relax program state
between the run.create() and eliminate() user functions, that would be
very useful. With the save state (and the relax version or SVN
revision being used) I will be able to head straight to the problem.
Thanks,
Edward
On 10/26/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
> Hi Edward,
>
> I've included the output from the log below, which is produced if the
> aforementioned lines are left commented out. If I uncomment them,
> the eliminate call does not report an error and the results files
> seem to contain the appropriate information. I'm not sure if it has
> anything to do with this, but my input rate files include residues
> with no rate information:
>
> 1 M
> 2 K
> 3 S 0.2907 0.0234
> ...
>
> It seems that relax must unselect residues 1 and 2 in the example
> above, so the determine_param_set_type definition in model-free.py
> fails unless the aforementioned lines are uncommented ... local_tm
> stays equal to 0, causing the problem with the inconsistencies check
> on lines 1033-1035.
>
> Doug
>
>
> #OUTPUT
> ... starting at the end of the log where the script is read in ...
> # The main class.
> Main(self.relax)
> ------------------------------------------------------------------------
> ----------------------------
>
> relax> run.create(run='local_tm', run_type='mf')
>
> relax> results.read(run='local_tm', file='results', dir='local_tm/
> aic', format='columnar')
> Opening the file 'local_tm/aic/results.bz2' for reading.
>
> relax> run.create(run='sphere', run_type='mf')
>
> relax> results.read(run='sphere', file='results', dir='sphere/round_5/
> opt', format='columnar')
> Opening the file 'sphere/round_5/opt/results.bz2' for reading.
> Loading all structures from the PDB file.
> Structure('../pdb/file.pdb'):
> Peptide chain of length 106
>
>
> relax> run.create(run='prolate', run_type='mf')
>
> relax> results.read(run='prolate', file='results', dir='prolate/
> round_5/opt', format='columnar')
> Opening the file 'prolate/round_5/opt/results.bz2' for reading.
> Using the structures from the run 'sphere'.
> Structure('../pdb/file.pdb'):
> Peptide chain of length 106
>
>
> relax> run.create(run='oblate', run_type='mf')
>
> relax> results.read(run='oblate', file='results', dir='oblate/round_8/
> opt', format='columnar')
> Opening the file 'oblate/round_8/opt/results.bz2' for reading.
> Using the structures from the run 'sphere'.
> Structure('../pdb/file.pdb'):
> Peptide chain of length 106
>
>
> relax> run.create(run='ellipsoid', run_type='mf')
>
> relax> results.read(run='ellipsoid', file='results', dir='ellipsoid/
> round_7/opt', format='columnar')
> Opening the file 'ellipsoid/round_7/opt/results.bz2' for reading.
> Using the structures from the run 'sphere'.
> Structure('../pdb/file.pdb'):
> Peptide chain of length 106
>
>
> relax> run.create(run='final', run_type='mf')
>
> relax> eliminate(run=None, function=None, args=None)
> RelaxError: All residues must either have a local tm parameter or not.
>
>
> Doug
>
> On Oct 25, 2007, at 5:05 PM, Edward d'Auvergne wrote:
>
> > Hi,
> >
> > This is quite a bizarre bug if uncommenting those lines fixed the
> > problem. Would you have the printout of the 'traceback' error message
> > of the failure? Or did the script fail without printing a message?
> > Do you have more information about the point of failure?
> >
> > These lines were commented out because they cause a fatal bug under
> > certain rare circumstances. But other code has developed in response
> > to this removal such that this test of spin system selection is not
> > necessary. This important function solely determines what type of
> > model-free analysis is being executed - local tm, diffusion tensor
> > optimisation, model-free optimisation for a single spin, or
> > optimisation of all parameters simultaneously. If uncommenting these
> > lines changes relax's behaviour, then the only reason is that not a
> > single residue is selected. Can you see this in any of your results
> > files? Or is there anything else suspicious with one of the results
> > files?
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > On 10/25/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
> >> Hi,
> >>
> >> The following comment is present on line 1021 in the specifc_fns/
> >> model-free.py file of the 1.2 svn version of relax:
> >>
> >> 1021 # This code causes a bug after model elimination if
> >> the model has been eliminated (select = 0).
> >> 1022 #if not self.relax.data.res[self.run][i].select:
> >> 1023 # continue
> >>
> >> The full_analysis.py script works find for the optimization of
> >> local_tm, sphere, etc ... but, I am unable to run the 'final' run in
> >> full_analysis.py unless I uncomment lines 1022-1023 in model-free.py.
> >>
> >> I have to manually uncomment these lines to run the final analysis,
> >> then comment out these lines again. Can the code in model-free.py be
> >> modified to something like this:
> >>
> >> if not self.relax.data.res[self.run][i].select and self.run ==
> >> 'final':
> >> continue
> >>
> >> Or should one not need to uncomment lines 1022-1023?
> >>
> >> Doug
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> relax (http://nmr-relax.com)
> >>
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>
>
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