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
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
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
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
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
participants (2)
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Elaine Meng
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Kavya Shankar