[chimera-dev] (no subject)

[Kavya Shankar]

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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