Does anyone know of a way to embed coordinates within a pymol script? I'd like to be able to programmatically generate a self-contained pymol script which loads the embedded coords, defines selections, and highlights selections with colors/rendering. The immediate use for this is to write a CGI which returns a pymol script over http. Thus, the coordinates cannot be expected to exist on the client side (and, in my case, are model coordinates, not a PDB entry).

RasMol provides the 'load pdb inline' command which loads a PDB file which appears at the end of the script. I'd like something similar for PyMOL, preferably generalized to multiple structures. An extension to load in which the filename could be '<<TAG' a la sh or perl (gasps heard on the list) would do the trick.

Reece Hart, Ph.D.        ,
Genentech, Inc.                    650-225-6133 (voice), -5389 (fax)
Bioinformatics and Protein Engineering
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