From owner-chemistry -x- at -x- ccl.net Mon May 10 11:53:00 2010
From: "Elaine Meng meng=cgl.ucsf.edu" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: Modify PDB file of DNA-Protein complexes
Message-Id: <-41836-100509131303-21822-dooTuAfihat7FlqG4NoVUg%server.ccl.net>
X-Original-From: "Elaine  Meng" <meng*_*cgl.ucsf.edu>
Date: Sun, 9 May 2010 13:13:01 -0400


Sent to CCL by: "Elaine  Meng" [meng||cgl.ucsf.edu]

Hi Deepangi,
You can do it with the "swapna" command in Chimera.

Chimera homepage:
http://www.cgl.ucsf.edu/chimera/index.html

Chimera manual:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html

manual page for "swapna":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html

Example commands:
open 1d86
nuc side atoms
swapna t :24.b

(that would open PDB 1d86, show all atoms of bases, 
and change the base of residue 24 in chain B to T)

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