Thanks for the answers. I'll be trying to get it compile on a linux box,
if I could access some of the PyMOL features there, that's fine as well.
A friend tried to compile PyMOL on Mac and had quite some trouble, so
I'll be first trying the Linux option.
Martin
Am 22.11.11 15:56, schrieb Jason Vertrees:
> Martin,
>
> The _cmd module is indeed statically linked into MacPyMOL. But, if you
> built from open-source it's dumped into site-packages/pymol. Also,
> view the files inside pymol/examples/launching. There are plenty of
> examples. If you're using a pre-built package from elsewhere, then
> please contact the package maintainer to see how it's built.
>
> Last, I prefer the newer "pymol2" strategy where you get a handle to a
> PyMOL cmd instance:
>
> from pymol2 import PyMOL
> cmd=PyMOL().cmd
>
> Cheers,
>
> -- Jason
>
> On Tue, Nov 22, 2011 at 8:19 AM, Thomas Holder
> <spel...@users.sourceforge.net> wrote:
>> 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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