[Chimera-users] Average structure

George Tzotzos gtzotzos at me.com
Mon Aug 3 09:19:50 PDT 2015

Thank you Elaine. Totally missed the format option. Really careless of me. Please accept my apologies


> On 3 Aug 2015, at 19:17, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi George,
> As per my earlier reply (below), MD Movie can just read PDB files, no topology file required.  You just have change the format option in the MD Movie input dialog.  The trajectory input format options including PDB are in a menu in the dialog and described here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> Elaine
>> On Aug 3, 2015, at 7:45 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> 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.
>> Regards
>> George
>> <pc1.pdb>
>>> 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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