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

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 29 10:10:44 PDT 2017

Hi Kavya,
I think I understood you, but I can only repeat the same answer.  I do not know of any way to get the axis  in Chimera except by first superimposing two copies of the dimer.  Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2.  Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.”  

> On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank at umail.iu.edu> wrote:
> Hi,
> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged.
> Thank you.
> Regards,
> Kavya Shankar
> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > 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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