Hi Vaheh,
* Oganesyan, Vaheh <oganesy...@medimmune.com> [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
<robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
