[Chimera-users] NMR

Elaine Meng meng at cgl.ucsf.edu
Mon May 7 09:47:34 PDT 2012

Hi Meshal,
In Chimera 1.7 (the development version, daily build) there is a new feature to calculate average coordinates.  To use this:

(1) get the daily build of Chimera.

(2) Start Chimera and open the NMR ensemble as a trajectory.  You can fetch the PDB file like you already did, but then save it to a single PDB file and close the structure.  Then re-open the single PDB file as a trajectory (start MD Movie from the Tools... MD/Ensemble Analysis menu, choose single-file PDB input format, browse to file location, open the file).

(3) In the MD Movie dialog menu, choose Analysis... Average structure. 

Note this is simple x,y,z coordinate averaging, and may produce a distorted structure. 

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

On May 5, 2012, at 12:51 AM, MESHAL ALMUALLIMI wrote:

> Hello, 
> How can I show only the average of my NMR solved structure? As when I fetch the PDBID 1YJR it shows all the structures aligned and I only need the average. I figured out how to eliminate as much structures as I can but I am interested in taking the average of all.
> Regards
> Meshal
> MS candidate
> Georgetown University

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