RE: [PyMOL] How to run PyMol from within Python?

[DeLano, W. <wa...@su...>]

> So there is no way to run and control PyMol from within=20
> another python program?

If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, =
then you can launch PyMOL from an external Python program as shown in =
examples/devel/start_pymol.py. =20

However, this is not recommended because the PyMOL launch sequence is =
not fixed.  If you do use it, be prepared to deal with changes down the =
road.=20

> The reason for asking is that we are working on a python platform to=20
> run and evaluate protein-protein docking calculations. It would be a=20
> nice feature to be able to call up interaction surfaces and=20
> protein-protein clusters for display  in PyMol and then interact with=20
> them from within our program.

> As things are now I'm forced to treat PyMol as I would treat any=20
> molecular graphics program, that is write macros macros for it. This=20
> is of course much less convenient and less flexible compared to=20
> running PyMol from within our python code.

> Has anyone been able to run and quit PyMol from within python without=20
> killing the interpreter? Is it possible? How?

The underlying source of the limitation here is that the GLUT and Tcl/Tk =
libraries which PyMOL uses do not support repeated set-up/take-down -- =
they are both static "global" systems which steal threads and never =
return.  Thus, while PyMOL is not inherently limited in this fashion, =
these building blocks which it employs are.  Eventually there will be =
versions of PyMOL which are both GLUT and TCL/Tk independent -- but not =
today.

Instead, I recommend using some kind of inter-process communication =
along with object serialization to pass data from your program into =
PyMOL.  Python makes this relatively easy, but you are looking at a =
little bit of development.

Sorry the news isn't better!

Warren