[Chimera-users] NMR

[Elaine Meng]

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.
<http://www.cgl.ucsf.edu/chimera/download.html#daily>

(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).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

(3) In the MD Movie dialog menu, choose Analysis... Average structure. 
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#averaging>

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

I hope this helps,
Elaine
----------
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