[Chimera-users] color by RMSD

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 3 09:36:40 PDT 2012

Hi Thomas,
Two general possibilities:

(A) If the RMSD is to be calculated by Chimera, you would need to superimpose the proteins to calculate the RMSD, then color by that value using Render by Attribute or command rangecolor.  However, after the coloring step you could move the proteins apart.  The RMSD calculation in Chimera uses CA atoms, so if you only have two proteins, the per-residue "RMSD" boils down to simply the CA-CA distance between the two proteins in the superimposed state.


(B) Alternatively, if the RMSD is calculated by some other program you could create an "attribute definition" file that lists the values, read the file into Chimera to assign the attribute values to residues (or atoms), and then color by your custom attribute the same way as in (A).  The attribute file format is quite simple, see description and examples:

However, method (A) is probably easiest if  the CA-CA distance is an acceptable measure.  Example using MatchMaker command (mm) to superimpose and show sequence alignment:

open 2gbp
open 2fw0
mm #0 #1 show true
   ... sequence alignment should appear, including RMSD histogram above the sequences ...

To define and apply the coloring, you could use Render by Attribute (see the attribute of residues named mavRMSD) or rangecolor, for example:

rangecolor mavRMSD min purple mid red max yellow

Then you can un-superimpose the structures, for example, with command: reset, or manually with the mouse.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 3, 2012, at 5:46 AM, Thomas Evangelidis wrote:

> Dear UCSF Chimera users and developers,
> Is it possible to color a pair of structures representing different stages of the thermodynamic cycle of a protein by the RMSD, without aligning them?
> thanks in advance,
> Thomas

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