Hi,
It is a curious bug. With a bug report with an attached relax save
state (https://mail.gna.org/public/relax-users/2007-10/msg00028.html),
I'll be able to determine exactly which diffusion model is causing the
problem. Don't forget to include which version of relax you are
using.
Thanks,
Edward
On Oct 27, 2007 3:31 PM, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>
> Hi Edward,
>
> I will try to get you this information before the end of the
> weekend. Cursorily, it seems the error occurs when data is missing,
> not at the beginning of the input rate files, but after (at least
> one) rate has been specified. That is, relax seems to work OK for
> this type of situation:
>
> (A)
> Num Name Value Error
> 1 M
> 2 Q 0.626 0.004
> 3 Y 0.633 0.004
> 4 K 0.646 0.004
>
> but not this type of situation (although this was not the exact case
> I tested):
>
> (B)
> Num Name Value Error
> 1 M
> 2 Q 0.626 0.004
> 3 Y
> 4 K 0.646 0.004
>
> although, I have not tested this situation:
>
> (C)
> Num Name Value Error
> 1 M
> 2 Q 0.626 0.004
> 4 K 0.646 0.004
>
> my input files follow a similar format to (B).
>
> Doug
>
>
>
> On Oct 26, 2007, at 12:21 PM, Edward d'Auvergne wrote:
>
> > 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)
> >>>>
> >>>> 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://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
