[Chimera-users] automated rebuilding of side chains?

Elaine Meng meng at cgl.ucsf.edu
Fri May 2 10:43:28 PDT 2008

Hi Ian,
Dock Prep now rebuilds  truncated sidechains using data from rotamer  
libraries (Dunbrack or Richardson):


It automatically locates the truncated sidechains, retrieves rotamer  
information, and chooses the best rotamer based on clashes, H-bonds,  
and (by default) backbone conformation.  This may take a while... it  
sounds like your system is pretty large. It will not add in missing  
backbone segments or entire residues, however, only sidechains.

Dock Prep was changed after the last production release (Nov 2007),  
so I recommend getting a daily build:

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 1, 2008, at 10:08 PM, Ian Yarbrough wrote:

> Hi,
> A model that I am working with has several missing or partial side  
> chains, and I'm dealing with about 80 subunits of this protein  
> (organized into 3 chains).  I am trying to repair these, but don't  
> want to go through the task of finding every broken chain.  Is  
> there a way to get chimera to locate the broken ones and repair  
> them all?  I've seen the dock prep feature, but don't want to  
> change them all to alanines.
> Thanks for you help.
> Ian Yarbrough
> Texas A&M University
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