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.kolstoe@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