[Chimera-users] Measuring rotation

Elaine Meng meng at cgl.ucsf.edu
Tue May 18 17:28:37 PDT 2021

Hi Javad,
The "measure rotation" command only measures the current transformation (rotation and translation) of a whole model relative to another whole model.  It does NOT tell you what transformation is needed to best superimpose their atoms. This is explained in the help for that command:

You would do the superpositioning/fitting yourself first, and THEN use measure rotation.  You can do the fitting with any method, manually by hand, or with Matchmaker to use backbone CA, or "match" to use only a specific residue or set of residues.  Furthermore for constant frame of reference you would probably want to measure the transformation of the same structure compared to itself, so if you are comparing the rotation of A and B, you would open A two times (A and A'), superimpose A onto B with your favorite method, and then measure rotation of A compared to A'.

This multi-step process may be confusing, so if possible you could try using just this single step: the "match" command, specifying whatever atoms you want to use for fitting, and include its "show true" option to report the transformation matrix in the Reply Log, and also "move false" if you don't actually want to move the structure.   For example, something like:

match #0 at ca #1 at ca move false show true
... to use all CA atoms

match #0:45.A #1:45.A move false show true
...to use all atoms of residue 45 in chain A

This alternative is also mentioned in "measure rotation" help link I gave above.

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

> On May 18, 2021, at 4:53 PM, JAVAD KARIMBAYLI <javad.karimbayli01 at universitadipavia.it> wrote:
> Greetings dear sir/madam
> I was trying to measure the rotation of my protein before vs after activation 
> using the "measure rotation #0 #1" command, which worked smoothly. 
> Then I wanted to check the rotation of specific residues. However, when I tried to specify residues, for example, residue 45 of model0 vs model1, the code didn't work. I have gone through Chimera documentation but didn't really find how to solve the issue.
> So, I kindly ask for your suggestions about how I may get residue-specific rotations.
> Thank you in advance
> Javad Karimbayli

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