[Chimera-users] Averaging multiple structures

Elaine Meng meng at cgl.ucsf.edu
Wed May 11 16:43:20 PDT 2016

Hi Yehuda,
To average the structures in Chimera, you need to open them as a trajectory with the MD Movie tool (in menu under Tools… MD/Ensemble Analysis).  This can be done even if they are separate PDB files but they would have to meet certain naming conventions; see the multiple-files PDB option in the “Startup and Input” section of the MD Movie manual page:


So you might need to rename your files.  Also I believe they would need to each contain the same set of atoms.

Once they are loaded as a trajectory, then see the “Structure Averaging” section of the manual page linked above.
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 11, 2016, at 4:35 PM, Yehuda Halfon <yehuda.halfon at weizmann.ac.il> wrote:

> Hi there, 
> I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. 
> Thanks, 
> Yehuda 

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