Re: [bug #12499] DIFF_MODEL = 'prolate' optimization failure -- October 24, 2008 - 21:39

No, I haven't seen that. However, is it possible that you need local_tm or
sphere data files? If you went back and started with local_tm and worked your
way to 'prolate,' I don't think that will replicate the error without 
the full,
unmodified, data set. I had to put file #4925 in the directory 
described in the
comment to replicate the error with the test set.

Tyler


Quoting Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>:

> I'm actually getting a different error at the start of the script.
> Tyler, have you seen the following message in your test data?
>
>
> ----------------------------------------------------------------------------------------------------
>
> relax> pipe.create(pipe_name='prolate', pipe_type='mf')
>
> relax> results.read(file='results', dir='local_tm/aic')
> Opening the file 'local_tm/aic/results.bz2' for reading.
> RelaxWarning: The structure file 'PDB_file.pdb' cannot be found in the
> current directory or the directory of the results file.
>
> relax> model_free.remove_tm(spin_id=None)
>
> relax> structure.read_pdb(file='PDB_file.pdb', dir=None, model=None,
> parser='scientific')
>
> Scientific Python PDB parser.
> Loading all structures from the PDB file.
> Structure('PDB_file.pdb', model=1):
>  Peptide chain A of length 1
>
>
> relax> structure.vectors(attached='H', spin_id=None,
> struct_index=None, verbosity=1, ave=True, unit=True)
> Extracting vectors from the single structure.
> Calculating the unit vectors.
> The attached atom is a proton.
>
> Traceback (most recent call last):
>  File "/data/relax/relax-1.3/relax", line 422, in <module>
>    Relax()
>  File "/data/relax/relax-1.3/relax", line 131, in __init__
>    self.interpreter.run(self.script_file)
>  File "/data/relax/relax-1.3/prompt/interpreter.py", line 270, in run
>    return run_script(intro=self.__intro_string, local=self.local,
> script_file=script_file, quit=self.__quit_flag,
> show_script=self.__show_script,
> raise_relax_error=self.__raise_relax_error)
>  File "/data/relax/relax-1.3/prompt/interpreter.py", line 531, in run_script
>    return console.interact(intro, local, script_file, quit,
> show_script=show_script, raise_relax_error=raise_relax_error)
>  File "/data/relax/relax-1.3/prompt/interpreter.py", line 427, in
> interact_script
>    execfile(script_file, local)
>  File "full_analysis.py", line 673, in <module>
>    Main(self.relax)
>  File "full_analysis.py", line 266, in __init__
>    structure.vectors(attached='H')
>  File "prompt/structure.py", line 498, in vectors
>  File "/data/relax/relax-1.3/generic_fns/structure/main.py", line
> 308, in vectors
>    if obj:
> ValueError: The truth value of an array with more than one element is
> ambiguous. Use a.any() or a.all()
>
> Regards,
>
> Edward
>
>
> On Fri, Oct 24, 2008 at 9:10 PM, Edward d'Auvergne
> <edward.dauvergne@xxxxxxxxx> wrote:
> > Hi,
> >
> > Would it be possible to add a quick comment to the bug detailing which
> > directory each file should be in?  I'm trying to reproduce the bug
> > now.
> >
> > Cheers,
> >
> > Edward
> >
> >
> >
> > On Fri, Oct 24, 2008 at 8:57 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> > > It seems the main thing to reproduce this bug is to have the file #4925 I
> > > uploaded in the prolate round1/opt directory where it is called 
> > > during the 2nd
> > > round.
> > >
> > > I truncated and changed a bunch of stuff, but it was all reproducible
> > > with this
> > > minimized set once the files are in the right places.
> > >
> > > Tyler
> > >
> > >
> > > Quoting Tyler Reddy <NO-REPLY.INVALID-ADDRESS@xxxxxxx>:
> > >
> > > > Additional Item Attachment, bug #12499 (project relax):
> > > >
> > > > File name: r2_500.out                     Size:0 KB
> > > > File name: r2_800.out                     Size:0 KB
> > > > File name: r2_600.out                     Size:0 KB
> > > > File name: sequence_input                 Size:0 KB
> > > >
> > > >
> > > >    _______________________________________________________
> > > >
> > > > Reply to this item at:
> > > >
> > > >  <http://gna.org/bugs/?12499>
> > > >
> > > > _______________________________________________
> > > >  Message sent via/by Gna!
> > > >  http://gna.org/
> > >
> > >
> > >
> > >
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