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/
>
>
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Re: [task #3838] Splitting up and redesigning the 'pdb()' user function.