Re: [PyMOL] APBS

[Robert C. <rob...@qu...>]

Hi Vaheh,

* Oganesyan, Vaheh <Oga...@Me...> [2007-05-30 09:45] wrote:
> I did not get much luck with those recommendations either. I was doing exactly the same. Something is phishy with my pymol and/or APBS installation. I did check for different pdb files, so it is not pdb related. The roor message is below:
> ==============================================================================================================
> Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs', '/home/Vaheh/Work/Fc3M/pymol-generated.in')
> OSError Exception in Tk callback
>   Function: <function <lambda> at 0xf608448c> (type: <type 'function'>)
>   Args: ()
> Traceback (innermost last):
>   File "/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__
>     return apply(self.func, args)
>   File "/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py", line 153, in <lambda>
>     command=lambda self=self, name=name: self._doCommand(name))
>   File "/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py", line 132, in _doCommand
>     return command(name)
>   File "/usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1101, in execute
>     (retval,progout) = run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),))
>   File "/usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py", line 317, in run
>     retcode = subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
>   File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 412, in call
>     return Popen(*args, **kwargs).wait()
>   File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 542, in __init__
>     errread, errwrite)
>   File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 975, in _execute_child
>     raise child_exception
> OSError: [Errno 8] Exec format error

                     ^^^^^^^^^^^^^^^^^^

This error would seem to indicate that you are running PyMOL on one kind
of computer but the apbs executable was compiled for a different one.
Are you perhaps mixing i686 and x86_64 Linuxes, for example?

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc