From owner-chemistry@ccl.net Thu Aug  2 13:26:00 2007
From: "Elaine Meng meng%%cgl.ucsf.edu" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34855-070802123838-28738-Rx7y7KsDN6qI5fqickdB6A*server.ccl.net>
X-Original-From: "Elaine  Meng" <meng||cgl.ucsf.edu>
Date: Thu, 2 Aug 2007 12:38:35 -0400


Sent to CCL by: "Elaine  Meng" [meng-$-cgl.ucsf.edu]
Hi Max,
Many programs add hydrogens, including the one I work on (Chimera,
http://www.cgl.ucsf.edu/chimera/ ).

Probably the easiest, however, if you would rather not get a program
you don't already have is to use the Richardson group's MolProbity
server:

http://molprobity.biochem.duke.edu/

You can upload a file or enter its PDB ID.  Just follow the steps;
there will be choices of what to do to the structure, including
adding hydrogens.  The hydrogen addition is high-quality and takes
local H-bonding patterns into account.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng---cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html