Try redirecting stderr and stdout to a file -- the process may be getting suspended by the shell due to output.
pymol -qc script.pml >& pymol.log
pymol -qc script.pml > pymol.log 2>&1

From: [] On Behalf Of Gordon Wells
Sent: Thursday, September 20, 2007 10:11 AM
Subject: [PyMOL] pymol in the background


I seem to be having trouble running pymol (v1.0, gentoo) in the background from a terminal, neither appending "&" nor "ctrl+z" followed  "bg" is doing the trick. In both cases pymol freezes during certain operations, eg opening pdbs, drawing cartoon. The window controls themselves respond. Don't want to have to change directory in pymol all the time. Any ideas?

I think perhaps the most important problem is that we are trying to understand the  fundamental workings of the universe via a language devised for telling one another when the best fruit is.

        -- Terry Pratchett,

Gordon Wells
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria