[Chimera-users] Bug (?) with EnsembleCluster
pett at cgl.ucsf.edu
Thu Jan 17 16:05:11 PST 2008
On Jan 16, 2008, at 8:19 AM, Francesco Pietra wrote:
> I was unable to find how to get a plot of RMSD against time. I
> would like to do
> that for the ligand (which is a single big residue) and selected
> residues of
> the protein.
Mmmm, RSMD compared to what? Frame 1?
You can't get such a plot right now, but what you can do is open your
trajectory and also open a PDB file with whatever structure you want
to measure RMSD with, and in the "Define script..." dialog put:
match #0<+atom spec you wanted compared> #1<+atom spec you want
Then if you play through the trajectory, in the reply log will be
pairs of lines like this:
which is the frame number and the RMSD.
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