Hi Daniel,
You say you used "split_states", so all your conformations have the same
topology (are the same molecule). In that case, I suggest to use cmd.rms
instead of cmd.align, which will be more efficient. You also don't need to
split the structures, but call the function with the correct
Hi!
I have a group of structures (168 in total) and I want to align all of them
to the first one in order to know the RMSD calculation. For that purpose I
use the following:
f=open('rmsd.txt','w')
rms2=cmd.align('structure_0002 and name ca','structure_0001 and name ca')
.
. (NOTE: I got all of
...@iitg.ernet.in
Sent: Wednesday, June 04, 2008 3:15 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RMSD Calculations
Hi everyone,
I needed to know how to calculate the RMSD for 2 homologous structures over
the entire structure (For C-alpha atoms). Currently, PyMol performs sequence
Hi everyone,
I needed to know how to calculate the RMSD for 2 homologous structures
over the entire structure (For C-alpha atoms). Currently, PyMol performs
sequence alignment and then gives the RMSD values for only those regions
which are matching. But, as I mentioned before, I need RMSD values
