Hello,
I have been looking at the archived discussions, and I have never seen a
single discussion that had any images.
Is it just archived transaction that is lacking images, or is it not
possible to attach images to this email?
Best,
Jun Ha Song.
3
2
Define Plane
by Catherine Jenifer Rajam Rajendran
01 Jul '17
01 Jul '17
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
