[Chimera-users] barycenter of a model

mljin jinmingliang2013 at sibcb.ac.cn
Tue Sep 12 06:30:51 PDT 2017


Dear Elaine,
I got another question here, I have two models, these two model are the same molecule but with different conformation. This molecule composes several subunits. And the conformation change include not only like subunit rigid body rotation but also a self movement, I would like to do a morph between these two, but actually I do not know how to put these two molecule in the Chimera, I mean the relative position, by which I can do morph and study the rigid body rotation and movement. I try to find the axis and the center of mass by your advice, however, I still need another valve to fix it in right position, because I only have a axis and a center, still lack a third vale, does there any method to solve this? 
Best regard!
Mingliang 

> 在 2017年9月12日,上午12:57,Elaine Meng <meng at cgl.ucsf.edu> 写道:
> 
> 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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