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 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)."
- 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?