[Chimera-users] Average structure

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 28 10:14:20 PDT 2015

Hi George,
You would have to use the MD Model tool.  However, if your “concatenated” PDB file is in the correct multi-model PDB format, you can just read in that file as the trajectory… no other files (topology etc.) needed.  See the “PDB, single file” input format option. 


The correct format is with MODEL and ENDMDL lines, such as used for NMR ensembles in the RCSB PDB repository (example: 1PLX).

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 Jul 28, 2015, at 8:22 AM, George Tzotzos <gtzotzos at me.com> wrote:
> Hi everybody,
> I’m analysing the Principal Components of an Amber trajectory. I have generated a number of representative pdb files which are concatenated for each PC.
> Question: Is there a way to generate an average structure in Chimera from the concatenated PDB files? 
> I know this can be done using MD movie but this solution requires that I generate a new topology file for my complex (the original topology file contains ligands and water molecules). 
> Thank you in advance for any suggestions
> Regards
> George

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