Hi,
I wrote a new PyMOL command a year ago to draw protein-ligand interactions
and create publication-quality images. Not exactly what you are looking for
but may be of help. It is already in the PyMOL script repository, so if you
have it you can load the command directly. For more details look at
Hi,
I do not provide a full solution...
I suggest
* try every particular step in pymol, in the command window
* if one step is successful, then put it (finally everything) into a file
* use python commands (not pymol; e.g. cmd.color("blue", "lig_01"))
* run the file either using "run python.file.
I have two receptors and their active sites for which I need to draw about
70 separate ligand-active site images (.png). Both active sites are saved
in session files (.pse) based on 3D coordinates from pdbqt files after
prepping for Vina docking. The ligand 3D coordinates are based on
*_out.pdbq
