[Chimera-users] barycenter of a model

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 11 09:57:15 PDT 2017


Dear Mingliang Jin,

(1) to find center of mass, see command “measure center”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>

If your model is an atomic structure, another possibility is “define centroid” with “massWeighting true” (otherwise it will find the center of geometry, treating all atoms equally):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>

(2) to find C2 symmetry axis of an atomic structure (not a map), you could try opening two copies of the structure, matching one half in one copy to the OTHER half in the other copy, and then measuring the axis of rotation between the two copies.  See this previous post with example commands for the structure 5hvp:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html>

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

> On Sep 11, 2017, at 1:26 AM, mljin <jinmingliang2013 at sibcb.ac.cn> wrote:
> 
> Dear USCF Chimera developers,
> 
> I got a question here, how to find the barycenter of a model in UCSF Chimera? 
> And the Model has a C2 symmetry, I can only find the symmetry axis.
> 
> Best regards,
> Mingliang Jin
> 
> NCPSS, SIBCB, CAS




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