[Chimera-users] calculate axes from centroids

[Elaine Meng]

On Nov 3, 2013, at 7:49 PM, Lili Peng <lilipeng at gmail.com> wrote:

> Hi Elaine,
> I've inquired you in the past regarding defining angles and planes in UCSF Chimera.
> Do you know if there's a way to define an axis through two centroids, or through the center-of-mass of a residue and the centroid of a subunit, some combination like that?
> Thank you,
> Lili
> 

Hi Lili,
Currently, axes (and planes and centroids) can only be calculated from sets of atoms, not centroids.

However, it can done in current Chimera by  defining centroids, adding fake atoms at their positions, and using those atoms to define axes.  You can specify whether each centroid calculation is mass-weighted (center of mass) or not (default, center of geometry).

(a) use Axes/Planes/Centroids (or command "define") to define the desired centroids
(b) look in Reply Log for the coordinates of each centroid
( c) add atoms: Tools… Structure Editing… Build Structure, Start Structure section, use settings to add atom with specific x,y,z coordinates to the existing model (the one whose atoms you used to define centroid)
(d) use new atoms to define axis

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

There is also a "measure center" command that will automatically create a fake atom (option "mark true"), so you could use that instead for steps a-c, but it always does mass-weighting.  For non-mass-weighted centroids, you would need to use the full process outlined above.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>

I hope this helps.  Sorry it is not as simple as it should be.
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco