[Chimera-users] Comparison of 2 structures

Elaine Meng meng at cgl.ucsf.edu
Sun Apr 21 09:47:01 PDT 2019

Hi Dmitry,
Your question is somewhat vague.  Of course you can use just about any atomic-structure analysis tool in Chimera on each structure (H-bonds, contacts, color surface by electrostatic potential and/or hydrophobicity, etc.) and thus compare the results.  However, there is no single “compare” command that is going to do all that for you in one step. You can also superimpose the structures and see where they are well superimposed vs. variable in structure. You can see it on the structures directly when they are superimposed, and also as an RMSD header shown above each column of a sequence alignment associated with the sequences. 

See superposition:

See tutorials and the atomic-structure analysis tools therein:

Superpositions and alignments (this describes the RMSD header above the alignment I mentioned above):

Structure analysis and comparison

Surface properties

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

> On Apr 20, 2019, at 4:02 AM, Dmitry A. Semchonok <semchonok at gmail.com> wrote:
> Dear colleagues,
> I have 2 similar structures that differs on the position of subunits.
> Do you know if Chimera can compare 2 structures and write a kind of report?
> Or is there any program that can do that?
> Both structures are in the pdb format
> Thank you.
> Sincerely,
> Dmitry

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