From owner-chemistry@ccl.net Tue Apr  6 14:21:00 2010
From: "Elaine C Meng meng()cgl.ucsf.edu" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: amino acid clashes
Message-Id: <-41609-100406133303-2781-LtriY4+D5vnyEXHa/FnwCg!=!server.ccl.net>
X-Original-From: "Elaine C Meng" <meng-$-cgl.ucsf.edu>
Date: Tue, 6 Apr 2010 13:32:54 -0400


Sent to CCL by: "Elaine C Meng" [meng.]|[.cgl.ucsf.edu]
Tania's question was already answered on the chimera-users]|[cgl.ucsf.edu mailing list, see

http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005007.html

To summarize, she should be using the option in Chimera's
Find Clashes/Contacts tool to ignore pairs of atoms 
that are directly bonded or separated by only a few bonds.
That option is on by default.  The bonded atoms are often
closer together than would be expected from their VDW radii
alone, and if that option is turned off, those pairs will often
be identified as clashing even though they are not really clashes.

Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco