[Chimera-users] Bug (?) with EnsembleCluster

Eric Pettersen 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:

echo <FRAME>
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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