[Chimera-users] Getting the median protein structure after comparing.

Elaine Meng meng at cgl.ucsf.edu
Sat May 29 17:26:58 PDT 2021

Hi Shradheya,
There is no built-in tool to do this.  You would first need to decide what is actually superimposed (how close, and which atoms should be used to evaluate that).  Then, in the unmatched parts, figure out which residue in one structure compares with which residue in the other structure.  If these are the same protein with same sequence, then it is easy.  If they are different proteins and/or there are gaps in the alignment, it is harder.  Then, find another program or write your own to average the coordinates of those unmatched parts.

If and only if the two structures are exactly the same protein with EXACTLY the same atoms, residues, numbering, etc.  in the same order, then you could possibly try the following in Chimera.

(1) Save both superimposed structures together as a single multi-model PDB file.  

(2) Open that single PDB file as trajectory with just two frames (Tools... MD/Ensemble Analysis... MD Movie, and in the input dialog choose PDB, single file, then browse to open the file you saved).  

(3) Then in MD Movie's menu, use "Analysis... Average structure"

That would average the whole thing, even the well-matched parts. 

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 29, 2021, at 12:31 PM, Shradheya R.R. Gupta <shradheyagupta at gmail.com> wrote:
> Hi,
> I have two PDB's I compared (superimposed) them using the Chimera tool. But some regions are not superimposed. 
> I want to generate the new PDB which have the superimposed regions coordinates and the median coordinates of the region which is not superimposed.
> Thank you

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