[Chimera-users] Structural matching of Side-chain selection

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 12 10:55:14 PDT 2016

Hi James,
No, because Matchmaker uses the sequences and only the CA atom per residue.   To calculate RMSDs for sidechain atoms in two structures, you could use either the “match” command or the “rmsd” command.  The difference between the two is that “rmsd” does not move the structures to superimpose them… it just uses their  current positions, so you will get a large number if the structures are far apart.

Summary of superposition methods in Chimera:
Manual pages for “match” and “rmsd”:

Or, if you wanted the least-squares fit RMSD (like the “match” command) but for several different frames from the MD simulation vs. the crystal structure, instead of using the match command several times, you can use the Ensemble Match tool (in menu under Tools… MD/Ensemble Analysis).  It is described as comparing two ensembles, but one of the ensembles could just be the single crystal structure.  The limitation, however, is that you would need to have exactly the same atoms with the same residue names and numbers in all of the structures you are comparing, which might be hard to achieve.

An example of using Ensemble Match is included near the end of the “Model Panel and Ensembles” tutorial:

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

> On Jul 12, 2016, at 7:11 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Dear Chimera users!
> I need to estimate how the side-chains dynamics are differs in MD
> compared to X-ray structure.
> Assuming that I have 2 structures one from md and another from X-ray
> and I select Sidechains from the both as obj1 and obj02 is it
> reasonable just to match them using MatchMAker?
> Thanks!
> James

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