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.
#
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
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,
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
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
