[Chimera-users] Average structure

[Elaine Meng]

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. 

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

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
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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