[Chimera-users] [chimera-dev] (no subject)

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 29 09:18:12 PDT 2017


> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank at umail.iu.edu> wrote:
> 
> Hi,
> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. 
> Thank you.
> Regards,
> Kavya Shankar

Hi Kavya,
Why not just match (superimpose) one monomer to the other and compare directly?   At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching.  However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis.  If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2).  This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

After two models are superimposed, you can get the axis and rotation amount with command “measure rotation”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>

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

P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues




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