Fwd: [task #3838] Splitting up and redesigning the 'pdb()' user function. -- October 13, 2006 - 16:21

---------- Forwarded message ----------
From: Alexandar Hansen <viochemist@xxxxxxxxx>
Date: Oct 13, 2006 10:18 AM
Subject: Re: [task #3838] Splitting up and redesigning the 'pdb()' user function.
To: Edward d'Auvergne <edward@xxxxxxxxxxxxx>

Diffusion models other than local_tm are not working.  My Traceback is:

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 193, in __init__
    pdb(name, self.alex_pdb)

AttributeError: PDB instance has no __call__ method

I ran the test-suite and also had some failures:

#############################
# Results of the test suite #
#############################

Angle calculation tests:
    The user function angles() .......................................................... [ Failed ]
   
    Mapping the {theta, phi, Da} chi2 space through the OpenDX user function dx.map() ... [ Failed ]


Synopsis ................................................................................ [ Failed ]


I just tried to do a 'svn up' to check my verision number and found:

svn: Malformed network data


Typing svn info I find that I have revision 2641.




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%
>
>
>     _______________________________________________________
>
> Reply to this item at:
>
>   <http://gna.org/task/?3838>
>
> _______________________________________________
>   Message sent via/by Gna!
>   http://gna.org/
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