We're getting there! The first run of each of the models finished, however
it was unable to load them for the next iterations. Here's the error I get
for ellipsoid (they're all the same though):
Traceback (most recent call last):
File "relax", line 458, in ?
Relax()
File "relax", line 170, in __init__
self.interpreter.run()
File "/local/home/viochem/relax/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 "/local/home/viochem/relax/prompt/interpreter.py",
line 388, in run_script
console.interact (intro, local, script_file, quit)
File "/local/home/viochem/relax/prompt/interpreter.py",
line 340, in interact_script
execfile(script_file, local)
File "full_analysis-ellipsoid.py", line 437, in ?
Main()
File "full_analysis-ellipsoid.py", line 227, in __init__
self.load_tensor()
File "full_analysis-ellipsoid.py", line 360, in load_tensor
results.read('tensor', 'results', self.diff_model + '/init')
File "/local/home/viochem/relax/prompt/results.py", line
122, in read
self.__relax__.generic.results.read(run=run, file=file,
directory=dir, format=format)
File "/local/home/viochem/relax/generic_fns/results.py",
line 132, in read
self.read_function(run, file_data, print_flag)
File
"/local/home/viochem/relax/specific_fns/model_free.py",
line 3404, in read_columnar_results
if self.read_columnar_pdb(print_flag):
File
"/local/home/viochem/relax/specific_fns/model_free.py",
line 3256, in read_columnar_pdb
self.relax.generic.pdb.load(run=self.run, file=pdb, model=pdb_model,
heteronuc=pdb_heteronuc, proton=pdb_proton, calc_vectors=0, fail=0,
print_flag=print_flag)
AttributeError: PDB instance has no attribute 'load'
Is this something I need to simply fix in my full_analysis scripts?
Otherwise, the first results.bz2 in the init/ files look fine. One question
though, is there some way to have it tell me Dratio instead of Da for
prolate and oblate? I know Da is your favorite, but it's confusing to me
and more difficult to physically understand (Drat = 5 means it's about 5
times longer than it is wide). I don't think there's an easy conversion
from Da to Dratio, is there?
Alex - Mr. RNA problem starter :)
On 10/26/06, Edward d'Auvergne <edward@xxxxxxxxxxxxx > wrote:
>
> I've completed a bit more work for this task and I think I now have
> everything functional. This includes revision r2668 which fixed the
> missing import of the re 'match' function, r2669 which fixed the names
> of the nucleic acids by stripping the letter 'R' prefixed by
> Scientific python, and r2670 in which the vectors calculated by the
> user function 'pdb.vectors()' were being overwritten if the function
> was called twice. The 'pdb' user functions now appear to work
> correctly. Alex, would you be able to have one last test of this? If
> you don't find any problems, I'll close the task.
>
> Edward
>
>
> On 10/4/06, Edward d Auvergne
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> >
> > URL:
> > < http://gna.org/task/?3838>
> >
> > Summary: Splitting up and redesigning the 'pdb()' user
> > function.
> > Project: relax
> > Submitted by: bugman
> > Submitted on: Wednesday 10/04/2006 at 08:32
> > Should Start On: Wednesday 10/04/2006 at 00:00
> > Should be Finished on: Saturday 10/14/2006 at 00:00
> > Category: None
> > Priority: 5 - Normal
> > Status: None
> > Privacy: Public
> > Assigned to: bugman
> > Percent Complete: 0%
> > Open/Closed: Open
> > Effort: 0.00
> >
> >
_______________________________________________________
> >
> > Details:
> >
> > The idea is to split the 'pdb()' user function back into the two
original
> > user functions 'pdb()' and 'vectors()'. All the details of this task
are
> > described in the post at
> >
https://mail.gna.org/public/relax-users/2006-10/msg00002.html
(Message-id:
> >
<7f080ed10610032153o4571935bq138d2739f55ca3bd@xxxxxxxxxxxxxx>).
> >
> >
> >
> >
> >
> >
> >
_______________________________________________________
> >
> > Reply to this item at:
> >
> > <http://gna.org/task/?3838>
> >
> > _______________________________________________
> > Message sent via/by Gna!
> > http://gna.org/
> >
> >
>
> _______________________________________________
> relax (http://nmr-relax.com )
>
> This is the relax-devel mailing list
> relax-devel@xxxxxxx
>
> 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-devel
>
Re: [task #3838] Splitting up and redesigning the 'pdb()' user function.