Subject: Re: [modeller_usage] Hydrogen Atom Preservation
From: Jonathan Sheehan <>
Date: Fri, 23 May 2014 16:31:33 -0500
Cc: Alexander Parella <>
Alexander,
The program Reduce from the Richardson lab (
http://kinemage.biochem.duke.edu/software/reduce.php ) does a good job
adding hydrogens to protein structures, and there are many other
modeling programs that can perform that step (some listed here:
http://kpwu.wordpress.com/2012/02/24/add-protons-hydrogens-to-structure/
).
Although these programs will not solve your problem if you must
*preserve* the locations of hydrogens in the structure you input to
Modeller, that requirement is relatively uncommon.
Hope that helps,
-J'n
--
Jonathan Sheehan, Ph.D.
Computational Structural Biology
Vanderbilt Univ. Ctr. for Struct. Biol.
5137 MRB3, 465 21st Avenue S.
Nashville, TN 37232-8755
615-936-2516