[Chimera-users] Average structure

George Tzotzos gtzotzos at me.com
Mon Aug 3 07:45:38 PDT 2015

Hi Elaine,

It seems that I’m stuck. I can open the attached file in Chimera. No problem with this. However, I cannot use the MD Model tool as it requires a topology file. As a consequence, I cannot generate an average structure as you suggested. Of course, a work around would be to generate a topology file but I thought there could be an easier way.

Your kind help will be appreciated.


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> On 28 Jul 2015, at 20:14, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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
> ----------
> 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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