[Chimera-users] define plane question

Steven Waldauer waldauer at pci.uzh.ch
Sat Mar 16 07:42:52 PDT 2013

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

Universität Zürich
Physikalisch-Chemisches Institut
Winterthurerstr. 190, CH-8057 Zürich

Tel:  +41 (0)44 635 44 66
Fax: +41 (0)44 635 68 38
E-Mail: waldauer at pci.uzh.ch

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