[Chimera-users] color by RMSD

Thomas Evangelidis tevang3 at gmail.com
Tue Apr 3 14:36:03 PDT 2012

Hi Elaine,

Many thanks for the detailed information! I have managed to use matchmaker
and save the RMSD values as you described in method (A), but the problem is
that MultialignViewer measures only the RMSD of the CA atoms that were used
in the alignment. In my case I want to align chains B of the two structures
but measure the RMSD between chains A. Is it possible to do that?

Thanks in advance for any help.


On 3 April 2012 19:36, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers
> >
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render
> >
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
> (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:
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile
> >
> 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 ...
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html>
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
> I hope this helps,
> Elaine
> ----------
> 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



Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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