[Chimera-users] centre of local mass

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 16 14:34:33 PDT 2016


Hi Kyle,
It seems all would depend on the definition of local.  Maybe you can mask or volume-erase or vop zone (around your current marker) to remove or zero the parts that you consider  to be nonlocal, then measure center of mass of the resulting map?  I don’t know how well that would work, however.

Related links:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>

I was also thinking about some kind of filtering or binning (e.g. other vop options), but that might reveal a low-res maximum rather than a center of mass.

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



On Mar 16, 2016, at 1:45 PM, Morris, Kyle <Kyle.Morris at warwick.ac.uk> wrote:

> Dear Chimera dev and community,
> 
> If I have approximately placed a marker into my volume density, is there a way to recentre this marker according to the centre of mass of the local density rather than the centre of mass of the whole volume?
> 
> Many thanks for your help!
> 
> Best wishes,
> Kyle




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