Hi Edward-
I am able to feed commands into PyMOL from Tcl/Tk scripts through the
use of UNIX pipes. From within the Tcl/Tk script, a pipe is opened
to PyMOL, and the script sends commands to PyMOL. I can tell PyMOL
to open a PDB file, display it in a certain way (cartoon, ribbon),
highlight certain atoms or residues (by sticks, spheres, etc.), color
them, etc. I've never tried writing images, but I don't think it
would be too difficult. Is this the type of functionality you are
looking to incorporate into relax?
Doug
On Oct 27, 2006, at 3:51 AM, Edward d'Auvergne wrote:
I use PyMOL as well, the graphics are much better. However I have
tried getting relax to interface with PyMOL but this has been
problematic. Essentially to access the internals of PyMOL, relax
would have to run within PyMOL's python prompt as a PyMOL plugin. The
same situation occurs with VMD. Molmol on the other hand can be
controlled from within relax.
To use these molecular viewers relax must be able to control them -
not the other way around where the viewers control relax (which, in
the case of PyMOL and VMD, is probably not too difficult). If someone
knows how to control PyMOL or VMD, or any other molecular viewing
program, to generate images using the data in relax, and would like to
add the feature into relax, that would very much be welcome. Much of
the code used to generate the Molmol images can be used to generate
images in other programs. The ultimate solution would be to have
PyMOL expose it's API to the command prompt or to expose it's python
interface to the prompt to allow relax to feed commands into it. Btw,
I'm not a fan of turning relax into multiple plugins for different
programs just to make this work.
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