Hi Ananya,
This is easily doable in PyMOL.
If you've already aligned the two structures and, let's stay they're
called protein1 and protein2, then use "rms_cur":
rms_cur protein1 and guide, protein2 and guide
If the initial and final structures are in the same object loaded from
disk then you
Dear all,
I have aligned two structures (one the initial structure and another one is the
final structure after MD simulation) in pymol, now I want to measure the
C-alpha- C-alpha distances of each residue between the initial and the final
structure of the MD simulation. Is it possible to do it
Excellent! I had previously been using things like 'not elem c+n+o+h+s' in
my scripts. Using 'metal' will match my intent much better. 'Sidechain'
will be appreciated as well.
I would suggest 'ligand' and 'ptm' selectors to distinguish nonbonded and
covalently bonded hetatms. Although I'm not sure
