[Chimera-users] define plane question

Elaine Meng meng at cgl.ucsf.edu
Sat Mar 16 09:14:32 PDT 2013

Hi Steven,
The "all helices" (protein) option is the only case where certain atoms are automatically used.

All other axis, plane, centroid calculations use whichever atoms you have specified in the define command (or if using GUI, whichever atoms are in the current selection).

I hope this helps,
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, 2013, at 7:42 AM, Steven Waldauer wrote:

> On Mar 15, 2013, at 10:42 PM, Eric Pettersen wrote:
>> To expand on the last bolded part:  the centroid is subtracted from the atoms and then eigenvectors/values are computed.  The eigenvector with the smallest eigenvalue is consider to be the normal to the plane (i.e. the two largest-valued eigenvectors define the plane).  A point (centroid) and a normal defines a plane.  The radius is as described in the first bolded section above.
> Thanks for the quick responses. I think I got it, but just to clarify, let me know if this is correct:
> The atoms in the selected residues are taken into consideration, and their coordinates are converted into a non-mass weighted centroid system. Then the principal axes are determined with the smallest vector considered normal to the plane defined by the other two axes.
> If this is correct, my only other question is: Which atoms are used in the calculation? Is it just N,CA,C like for helices?
> Thanks again for all the help.
> ******
> Steven Andrew Waldauer Ph.D.
> Postdoctoral Fellow, Hamm Group

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