Hi Martin,
I don't have a Mac so I can't test this, sorry.
I suspect that the _cmd module is built into the MacPyMOL executable.
This would imply that you cannot use MacPyMOL like in the
"Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users
knows more?
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 13:14:
> Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
>
> me @ ~/PROG_TEST $ python
> Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> imported numpy
> from PyQt4.QtGui imported *
> from PyQt4.QtCore imported *
>>>> import os, sys
>>>> import readline
>>>> import rlcompleter
>>>> readline.parse_and_bind('tab: complete')
>>>> moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
>>>> sys.path.insert(0, moddir)
>>>> os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
>>>> import pymol
> Traceback (most recent call last):
> File "<stdin>", line 1, in<module>
> File
> "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py", line
> 472, in<module>
> import _cmd
> ImportError: No module named _cmd
>>>> import pymol
>
>
> What could be the problem? Could it be that the 'pymol/pymol_path' call
> is not exactly right? In the modules/pymol directory, there is a module
> 'pymol/launch_pymol', but I have a similar error ("No module named
> _cmd") when I try to import it.
> Martin
>
>
>
>
>
>
> Am 22.11.11 09:47, schrieb Thomas Holder:
>> Hi Martin,
>>
>> the recommended way is to use PyMOL as your python interpreter, so
>> instead of:
>>
>> python file.py
>>
>> do this:
>>
>> pymol -cqr file.py
>>
>>
>> However, launching a PyMOL process from a python terminal as you
>> suggested is also possible. Have a look at Example 2 of
>> http://pymolwiki.org/index.php/Launching_From_a_Script , the important
>> lines are those:
>>
>> import pymol
>> pymol.pymol_argv = ['pymol','-qc']
>> pymol.finish_launching()
>>
>> Cheers,
>> Thomas
>>
>>
>> Martin Hediger wrote, On 11/22/11 09:26:
>>> Dear PyMOL List
>>> It comes up once in a while, is it possible to use PyMOL features
>>> from outside of PyMOL? An example, the below is a script (inspired by
>>> Thomas Holder) which saves down to disk all amino acids of a protein
>>> structure into separate PDB files.
>>>
>>> # *****************************************************************
>>> from pymol import cmd
>>> from pymol import stored
>>> from pymol.exporting import _resn_to_aa as one_letter
>>> # *****************************************************************
>>> def seq(state, selection="name ca or resn hoh or resn lig"):
>>> print "Generating seqs."
>>> cmd.select("prot", selection)
>>> while cmd.pop("_tmp", "prot"):
>>> cmd.iterate("_tmp", "stored.x=(resn,resv)")
>>> #print stored.x[0], stored.x[1]
>>>
>>> # Special case 1: Waters.
>>> if stored.x[0] == 'HOH':
>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>> # Special case 2: Substrate.
>>> elif stored.x[0] == 'LIG':
>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>> # Other: protein back-bone.
>>> else:
>>> filename = 'seq-%s%d-%s.pdb' %
>>> (one_letter[stored.x[0]].lower(), stored.x[1], state)
>>> cmd.save(filename, "byres _tmp")
>>> cmd.delete('_tmp prot')
>>>
>>> cmd.extend('seq', seq)
>>> # -----------------------------------------------------------------
>>>
>>> Is it possible to somehow include this in a Python script, and
>>> running it from the command line? If not, why?
>>>
>>>
>>> Thanks for any feedback.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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