[Chimera-users] An NMR Average Structure

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 21 10:03:31 PST 2007

Hi Simon,
Currently Chimera does not calculate an average structure from an  
ensemble, sorry.

This ability might be added in the future, but there are some issues:
If you simply average cartesian coordinates, the result is a somewhat  
distorted structure.  I'm told by my NMR colleagues that usually  
either this "average structure" is energy-minimized, or it is just  
compared to the existing ensemble members in order to select the most  
representative member.  The representative member rather than the  
"average structure" would then be used in further calculations.

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 Feb 20, 2007, at 9:11 AM, S W Simon Sham wrote:

> Hi,
> I need to calculate an average structure from an emsembled  
> structures in Chimera. Can we do it it Chimera? If yes, how?
> Thanks for any helps.
> Simon
> ---------------------------------------------------------------------- 
> -------
> Simon Sham, Ph.D.
> NMR Core Facility
> Comprehensive Cancer Center
> Univerisity of Alabama
> 933 South 19th Street
> CH19 B31
> Birmingham, AL 35294
> Office: (205) 934-5696
> Fax   : (205) 934-6475
> Email : ssham44 at uab.edu
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