# [Chimera-users] define plane question

Eric Pettersen pett at cgl.ucsf.edu
Fri Mar 15 14:42:25 PDT 2013

```On Mar 15, 2013, at 11:32 AM, Elaine Meng wrote:

> Forgot to mention the plane center and radius.
>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#plane>
>
> "The disk center is the non-mass-weighted centroid of the atoms; disk radius can be set to a fixed value as described below or set automatically to enclose the projections of the atoms (default). An extra margin (padding, default 0.0 Å) can be added to the automatically determined radius, but is ignored if a fixed radius is supplied."
>
> On Mar 15, 2013, at 11:25 AM, Elaine Meng wrote:
>
>> Hi Steven,
>> I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations.
>>
>> Axes/Planes/Centroids:
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
>>
>> "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).

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.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu

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