CCL: amino acid clashes

["Elaine C Meng" <meng-$-cgl.ucsf.edu>]

 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