On Tue, 2007-05-08 at 10:30, Carl Diehl wrote:
> Hi Edward.
>
> This was maybe a too hasty bug submit, since this problem doesn't appear
> in relax v1.3 which I installed after this version didn't work. But I'll
> test the fixes anyway.
> Cheers
> Carl Diehl
> Biophysical Chemistry, Lund University
>
> On Tue, 2007-05-08 at 00:00, Edward d'Auvergne wrote:
> > Hi,
> >
> > I have now fixed the bug. Carl, would you be able to test the fixes?
> > I unfortunately cannot replicate the bug as the relaxation data you
> > use is not available (however if absolutely necessary I could extract
> > it from the saved file). To check it you need the program Subversion
> > installed and then either type:
> >
> > svn co svn://svn.gna.org/svn/relax/1.2 relax-1.2
> >
> > or:
> >
> > svn co http://svn.gna.org/svn/relax/1.2 relax-1.2
> >
> > The resultant code in the 'relax-1.2' directory can then be directly
> > run using the script. I'll attempt a fix for your other bug report
> > and then maybe release relax-1.2.11.
> >
> > Cheers,
> >
> > Edward
> >
> >
> > On 5/7/07, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> wrote:
> > > Hi Carl,
> > >
> > > I'm sorry about the delayed response. I have just moved from
> > > Australia to Germany to start a postdoc and have been too busy to
> > > reply to any email until now. Thank you for the bug report. I've
> > > tried replicating the bug you have identified using your attached
> > > files but unfortunately I have recently upgraded my system and
> > > realised that relax doesn't function using Python 2.5. The relax
> > > error system is completely broken. I'll fix that then try to fix your
> > > problem.
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > >
> > > On 4/25/07, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> > > >
> > > > URL:
> > > > <http://gna.org/bugs/?8996>
> > > >
> > > > Summary: Bugs in palmer.py
> > > > Project: relax
> > > > Submitted by: None
> > > > Submitted on: Wednesday 04/25/2007 at 12:32 CEST
> > > > Category: relax's source code
> > > > Severity: 3 - Normal
> > > > Priority: 5 - Normal
> > > > Status: None
> > > > Privacy: Public
> > > > Assigned to: None
> > > > Originator Name: Carl Diehl
> > > > Originator Email: carl.diehl@xxxxxxxxx
> > > > Open/Closed: Open
> > > > Discussion Lock: Any
> > > > Release: 1.2.10
> > > > Operating System: GNU/Linux
> > > >
> > > > _______________________________________________________
> > > >
> > > > Details:
> > > >
> > > > The following bug were encountered while running the palmer.py script
with
> > > > stage=2, stage=1 worked fine with the original data.
> > > >
> > > >
> > > > relax> run.create(run='aic', run_type='mf')
> > > >
> > > > relax> model_selection(method='AIC', modsel_run='aic', runs=None)
> > > > AIC model selection.
> > > >
> > > > Instance 0.
> > > >
> > > > Run Num_params_(k) Num_data_sets_(n) Chi2
> > > > Criterion
> > > >
> > > > The model from the run None has been selected.
> > > >
> > > > Instance 1.
> > > >
> > > > Run Num_params_(k) Num_data_sets_(n) Chi2
> > > > Criterion
> > > > m1 1 6 4.17590
> > > > 6.17590
> > > > m2 2 6 3.77440
> > > > 7.77440
> > > > m3 2 6 4.17590
> > > > 8.17590
> > > > m4 3 6 3.77440
> > > > 9.77440
> > > > m5 3 6 6.09960
> > > > 12.09960
> > > >
> > > > The model from the run 'm1' has been selected.
> > > >
> > > > relax> results.write(run='aic', file='results', dir='aic', force=1,
> > > > format='columnar', compress_type=1)
> > > > Opening the file 'aic/results.bz2' for writing.
> > > > Traceback (most recent call last):
> > > > File "/home/matsl/carl/apps/relax-1.2.10/relax", line 454, in ?
> > > > Relax()
> > > > File "/home/matsl/carl/apps/relax-1.2.10/relax", line 166, in
__init__
> > > > self.interpreter.run()
> > > > File "/home/matsl/carl/apps/relax-1.2.10/prompt/interpreter.py",
line 213,
> > > > in run
> > > > run_script(intro=self.relax.intro_string, local=self.local,
> > > > script_file=self.relax.script_file, quit=1)
> > > > File "/home/matsl/carl/apps/relax-1.2.10/prompt/interpreter.py",
line 388,
> > > > in run_script
> > > > console.interact(intro, local, script_file, quit)
> > > > File "/home/matsl/carl/apps/relax-1.2.10/prompt/interpreter.py",
line 340,
> > > > in interact_script
> > > > execfile(script_file, local)
> > > > File "palmer.py", line 132, in ?
> > > > exec_stage_2(runs)
> > > > File "palmer.py", line 85, in exec_stage_2
> > > > results.write(run=name, file='results', force=1)
> > > > File "/home/matsl/carl/apps/relax-1.2.10/prompt/results.py", line
201, in
> > > > write
> > > > self.__relax__.generic.results.write(run=run, file=file,
directory=dir,
> > > > force=force, format=format, compress_type=compress_type)
> > > > File "/home/matsl/carl/apps/relax-1.2.10/generic_fns/results.py",
line 166,
> > > > in write
> > > > self.write_function(results_file, run)
> > > > File
"/home/matsl/carl/apps/relax-1.2.10/specific_fns/model_free.py", line
> > > > 4980, in write_columnar_results
> > > > self.write_columnar_line(file=file, num=data.num, name=data.name,
> > > > select=data.select, data_set='error', nucleus=nucleus, model=model,
> > > > equation=equation, params=params, param_set=self.param_set, s2=s2,
s2f=s2f,
> > > > s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r,
csa=csa,
> > > > diff_type=diff_type, diff_params=diff_params, pdb=pdb,
pdb_model=pdb_model,
> > > > pdb_heteronuc=data.heteronuc, pdb_proton=data.proton, xh_vect=xh_vect,
> > > > ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels,
frq=frq,
> > > > ri=ri, ri_error=ri_error)
> > > > AttributeError: Element instance has no attribute 'heteronuc'
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________________
> > > >
> > > > File Attachments:
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > Date: Wednesday 04/25/2007 at 12:32 CEST Name: palmer.py Size: 4kB
By:
> > > > None
> > > >
> > > > <http://gna.org/bugs/download.php?file_id=2268>
> > > > -------------------------------------------------------
> > > > Date: Wednesday 04/25/2007 at 12:32 CEST Name: stage1.save.bz2
Size: 3kB
> > > > By: None
> > > >
> > > > <http://gna.org/bugs/download.php?file_id=2269>
> > > >
> > > > _______________________________________________________
> > > >
> > > > Reply to this item at:
> > > >
> > > > <http://gna.org/bugs/?8996>
> > > >
> > > > _______________________________________________
> > > > Message sent via/by Gna!
> > > > http://gna.org/
> > > >
> > > >
> > > > _______________________________________________
> > > > relax (http://nmr-relax.com)
> > > >
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Re: [bug #8996] Bugs in palmer.py