[Chimera-users] Define Plane

[Catherine Jenifer Rajam Rajendran]

Hi,

I am trying to understand how the plane is defined in chimera. Can you
please help me with that?

"Define a plane for the specified
<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
atoms.
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)."

Define a plane for the specified
<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
 atoms.
- specified atoms, i use 'sel protein'

Eigenvectors/values are calculated from the atomic coordinates
- atomic coordinates, so x,y,z coordinates of all atoms. (Can you please
explain a bit more like how and what you read from PDB file to define
plane).

after subtracting the position of their non-mass-weighted centroid
- how is non-mass-weighted centroid is calculated

The plane is anchored at the centroid
- which centroid is this? Is the protein moved to the origin(0,0,0)
position?


Thanks,
Catherine
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170629/9f1a4b75/attachment.html>