Simon, You're triggering some special-purpose annotated PDB code from many years back. Are there USER records in your PDB files by chance? Getting rid of those should solve the problem.
Cheers, Warren -----Original Message----- From: Simon Kolstoe [mailto:s.kols...@ucl.ac.uk] Sent: Fri 3/27/2009 7:16 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Scripting question Dear PyMOL list, I am trying to visualise 20 docked ligand conformations using PyMOL. I have been opening PyMOL as the GUI, setting up a view of my protein, and then running the following script to load my ligand conformations: load conformer000.pdb, conf0 load conformer001.pdb, conf1 load conformer002.pdb, conf2 etc... However the script seems to also invoke the following commands which screw up my pretty picture: PyMOL>show cartoon PyMOL>util.cbac Executive: Colored 9 atoms. Executive: Colored 2 atoms. PyMOL>set cartoon_discrete_colors,1 Setting: cartoon_discrete_colors set to on. PyMOL>set cartoon_smooth_loops, 0 Setting: cartoon_smooth_loops set to off. PyMOL>set cartoon_flat_sheets, 0 Setting: cartoon_flat_sheets set to off. PyMOL>set valence,1 Setting: valence set to on. PyMOL>set stick_ball,1 Setting: stick_ball set to on. PyMOL>orient PyMOL>context_info=m4x.get_context_info() PyMOL>m4x.setup_contexts(context_info) Is there anyway of making the script JUST load the conformations and not change these other settings? Thanks, Simon ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
