[Chimera-users] define plane question

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 15 11:25:24 PDT 2013

Hi Steven,
I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations.


"Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the coordinates (prior to any helical correction)."  There is also a choice of mass-weighting or not.  If you choose the each-helix option, it is only using the backbone atoms N,CA,C.

The plane is the best-fit plane to the specified points (atoms).  

Maybe Eric can clarify if more details are needed, however.
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 15, 2013, at 10:53 AM, Steven Waldauer wrote:

> Hi Everyone,
> Hopefully this isn't a stupid question.
> I've used the define plane command for a few residues of slightly twisted beta-strand, trying to judge the distance and twist in relation to a helix across the binding groove at different conditions. It seems to work the way I would like it to, but I would like to know in more specific terms, how the plane is actually determined. When the structure measurements data is saved, the file returns the center coordinate, normal vector, and the radius. Could anyone tell me how these values are determined?
> For define axes, I can follow references from ksdssp, but there's really no similar definition for the define plane command in the user documentation.
> Thanks,
> Steve

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