Thank you, Elaine! On Mon, Nov 7, 2016 at 12:50 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Kavya, From <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#planes>:

"Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)."

Only the atoms you have selected are used in the calculation. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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On Nov 7, 2016, at 9:39 AM, Kavya Shankar <kavshank@umail.iu.edu> wrote:

Hi,

My thesis is on protein symmetry and I have been using the chimera's "Axes/Plane/Centroid" feature a lot. May I know what algorithm is being used in order to get the plane?

Thanks.

Regards, Kavya Shankar