[Chimera-users] Comparing 2 similar structures

Elaine Meng meng at cgl.ucsf.edu
Tue May 19 08:19:48 PDT 2020

Hi Dmitry,
The short answer is no.  There are bits and pieces for which ChimeraX or Chimera could be useful.

For listing the chains and what they are, and the HET residues and what they are, ChimeraX shows this in the Log automatically when you open a structure from the PDB (mmCIF or PDB).  Of course, you could get the same information by looking at the page for that entry at the RCSB PDB website.  Chimera lists the chain IDs and the HET residue names in the Select menu, but without their longer molecular names.

The compare part would be a lot trickier because it's not just comparing chemical entity but also spatial positioning.  E.g. if there were more than one copy of the same protein chain, which copy in one structure corresponds to the copy in the other structure?  And likewise for any bound HET residues. All I can say is to superimpose the structures with matchmaker (in either Chimera or ChimeraX) to figure that out.

ChimeraX can show a chain-chain contact diagram for each structure with the "interfaces" command, which may help in the comparison.

If you are just comparing one chain of the same molecular entity (same protein) in two or more structures, then in Chimera you could: associate them all with the full sequence (of any one of those chains, show using menu: Favorites... Sequence) in the Multalign Viewer tool.  To associate structures, see Multalign Viewer menu: Structure... Associations. Then from the associations list for the sequence (Multalign Viewer menu: File... Save Association Info) you can see which structures are missing which residues, and from the "RMSD:ca" header over the sequence you can get the CA-RMSD distance among all residues at each position of the sequence.  For two structures this boils down to just the CA-CA distance.  This sequence header is automatically assigned as a residue attribute of the associated structures, so you can color structures by it, write it out to a file, etc.

Multalign Viewer:
RMSD headers:

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

> On May 19, 2020, at 7:47 AM, Dmitry A. Semchonok <semchonok at gmail.com> wrote:
> Dear colleagues,
> I want to compare 2 models that have some differences: the same subunits but repositioned, missing structures, etc.
> Is there a tool in Chimera that can:
> -          Make a list of structure A (all components/residues). A list of elements in Structure B.
> -          Compare and report the missing parts in structure B compared to structure A? Maybe also the differences in distances between the same helices in structure B compared to structure A?
> Thank you!
> Sincerely,
> Dmitry

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