[Chimera-users] color by RMSD

Eric Pettersen pett at cgl.ucsf.edu
Mon Sep 10 15:06:11 PDT 2012

On Sep 7, 2012, at 1:19 PM, Daniel Gurnon wrote:

> Hi everyone,
> To color a trajectory by RMSD, comparing each frame to the final frame. My approach was to save the last frame of the trajectory as a pdb, load it as a separate model, and then run something like this script:
> mm #0 #1 show true
> rangecolor mavRMSD min white mid pink max red
> This works, but of course my screen quickly fills with multialign-viewer windows. Without "show true" in the script, coloring doesn't work past the first frame. Is there a way to do this without displaying the MAV window?

Hi Dan,
	The way Chimera is currently structured, there is no way to get that RMSD attribute assignment without creating the MAV window.  Now I could give you a script that closes the open MAV windows, which you could insert into your per-frame commands, but if I'm going to give you a script I might as well give you one that entirely bypasses the matchmaker/mav steps (which do a lot more work than strictly necessary for your purposes).  I've attached such a script.  Assuming you saved that script into the "Documents" folder of your home directory, your per-frame command would change to:

runscript ~/Documents/md-rmsd.py
rangecolor trajRMSD min white mid pink max red

As you might surmise from the rangecolor command above the script defines a "trajRMSD" attribute.  Also, I think you want to use actual specific numeric values rather than min/mid/max, since even matching against the reference frame can produce small numeric differences (due to PDB precision roundoff) which will nonetheless look just as big as much larger differences elsewhere in the trajectory.
	Now, I'm not certain for what purpose you are making this RMSD depiction, but I thought I should point out that in the daily build you can plot the RMSD difference for any set of atoms in a particular frame against the rest of the trajectory.  That feature is in MD Movie's Analysis->Plot menu.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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