Okay, it seems that "set auto_zoom, off" does work for PDB files, but not for SDF files. I have a python script that gives these three commands:
set auto_zoom, off load gsk_77553_l.sdf show sticks, gsk_77553_l But when you call the script, this is what happens in pymol PyMOL>set auto_zoom, off Setting: auto_zoom set to off. PyMOL>load gsk_77553_l.sdf Executive: object "gsk_77553_l" created. PyMOL>zoom (gsk_77553_l) PyMOL>show sticks, gsk_77553_l
