Dear Matt, There is a straighter way to do it. Try just
pymol.com pymol_script.pml (This works at least on my Linux machine). You can also try cat pymol_script.pml | pymol.com -p or even tail -f pymol_script.pml | pymol.com -p The latter allows one to append lines to the pymol script from an external program, which will be executed immediately. Kristian > I'm trying to use pymol to render a large number of complex images in > order to make a molecular movie. .. > > However, I'm having trouble getting the command mode to function. It > appears that one should launch pymol like so: > > pymol.com -c < pymol_script > > where "pymol_script" is a script file that you could otherwise invoke > from the GUI's command line by "@pymol_script". However, when I try > this with a simple script like:
