Paul,
 
Thank you for that bug report!  The command:
 
extract waters, solvent
 
solves the problem by pulling solvent atoms out into a separate object (named "waters").
 
Cheers,
Warren
 


From: Paul Mcewan [mailto:Paul.Mcewan@nottingham.ac.uk]
Sent: Friday, March 13, 2009 5:01 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] side chain helper

Dear all,
I'm currently using PyMol v1.2b2 and think I may have found a little glitch. While preparing a figure with waters and stick representations on a cartoon backbone with the sidechain helper switched on the sphere representation of the waters disappear leaving only nonbonded crosses. If there is any trick (other than blending the images in photoshop) to get around this could you let me know.
 
Thanks,
Paul..
 
###################################
Dr. Paul A. McEwan
Office B55
Centre for Biomolecular Science
University of Nottingham
Nottingham
NG7 2RD
UK
Tel: 0115 8232010 (office)
Tel: 0115 8232011 (lab)
http://www.nottingham.ac.uk/pharmacy/research/medicinal-chemistry-structural-biology/structbio.php
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