[Chimera-users] Averaging multiple structures

Yehuda Halfon yehuda.halfon at weizmann.ac.il
Wed May 11 17:14:31 PDT 2016


I found how to do it.

I load all the files. 
Remove the hydrogens and save them together as one PDB. 
Load it in MD Movie tool and run the average on it (since it has all the PDBs in it).
Then I save the new PDB.

Thanks a lot,

Yehdua
________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, May 12, 2016 3:10 AM
To: Yehuda Halfon
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Averaging multiple structures

Is that a question?  :-)

Deleting hydrogens is easy (e.g. command “delete H”) but I believe the other thing requires editing the file(s) outside of Chimera… should be pretty easy to script in whatever is your favorite scripting approach, though.

Elaine


On May 11, 2016, at 5:05 PM, Yehuda Halfon <yehuda.halfon at weizmann.ac.il> wrote:

> Hi Elaine,
>
> Thanks, it works fine.
> Now I just need to remove all the hydrogens from the PDBs and make sure the files ends with TER and not END.
>
> Yehuda
> ________________________________________
> From: Elaine Meng [meng at cgl.ucsf.edu]
> Sent: Thursday, May 12, 2016 2:43 AM
> To: Yehuda Halfon
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Averaging multiple structures
>
> 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:
>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
>
> 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
> -----
> 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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