[Chimera-users] Measuring rmsd without having exact number of atoms

Elaine Meng meng at cgl.ucsf.edu
Fri May 7 13:23:45 PDT 2021

Hi Ahmad,
There is no use in building missing parts to measure RMSD since they aren't in the "real" (known) structure anyway.  You just have to specify atoms that are already in both structures, which as you know, can be difficult and tedious.  Do not average multiple RMSD calculations (that defeats the purpose of calculating RMSD); instead, just do one RMSD calculation over the whole set of atom pairs. 

E.g. if segments 1-3 and 48-58 are missing from either/both of  two proteins with 131 residues (and assuming their numbering is the same), to match backbone atoms N,CA,C,O in chains A, it would be something like

match #0:4-47.A,59-131.A at n,ca,c,o  #1:4-47.A,59-131.A at n,ca,c,o

...or CA atoms only would be something like

match #0:4-47.A,59-131.A at ca  #1:4-47.A,59-131.A at ca

... with RMSD reported in the Log.  You could also try omitting the atom names if you think the residues all have all their sidechain atoms and you want to use them, but often that is not the case.

How would you figure out which residues are in both structures?  You may need to use a text-editor to look through the PDB files' ATOM lines to figure it out, and/or the Sequence view might also help.

match command:

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

> On May 7, 2021, at 12:48 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> Hi,
> Is there a work around measuring rmsd between two structures of the same protein, with one of them missing some segments, without having to rebuild / model the missing parts?!
> I'm thinking of writing a quick script to check for the matching segments, calculate rmsd for those and take an average of these measurements, unless there's a quicker way to do it! 
> Regards. 
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