Re: [task #3838] Splitting up and redesigning the 'pdb()' user function. -- October 13, 2006 - 16:29

That's my bad ... I forgot to use pdb.read(....) instead of pdb( .... ).

However, Now I'm getting this traceback error for diffusion models not local_tm:

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-sphere.py", line 437, in ?
    Main()
  File "full_analysis-sphere.py", line 194, in __init__
    pdb.vectors(name, heteronuc=self.alex_het1
, proton=self.alex_hyd1, res_name=self.alex_res1)
  File "/local/home/viochem/relax/prompt/pdb.py", line 202, in vectors
    self.__relax__.generic.pdb.vectors(run=run, heteronuc=heteronuc, proton=proton, res_num=res_num, res_name=res_name)
TypeError: vectors() got an unexpected keyword argument 'run'


Alex

On 10/13/06, Edward d'Auvergne < edward@xxxxxxxxxxxxx> wrote:

Alex, would you be able to test these new user functions on RNA?  Do
they work for you if you use the lines

pdb.read(name, self.alex_pdb)
pdb.vectors(name, heteronuc='N1', proton='H1', res_name='G')
pdb.vectors(name, heteronuc='N3', proton='H3', res_name='U')

in you relax script?  These changes are solely within the 1.3 repository line.

Your original post asking about this is located at
https://mail.gna.org/public/relax-users/2006-10/msg00001.html
(Message-id: <481156b20610031057k263a23act6aa2bb6729edf9a1@xxxxxxxxxxxxxx>).

This solution was discussed at post at
https://mail.gna.org/public/relax-users/2006-10/msg00002.html
(Message-id: <7f080ed10610032153o4571935bq138d2739f55ca3bd@xxxxxxxxxxxxxx >).

Thanks,

Edward


On 10/6/06, Edward d Auvergne <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
>
> Update of task #3838 (project relax):
>
>                   Status:                    None => Ready For Test
>         Percent Complete:                      0% => 100%
>
>
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