[Chimera-users] Color by RMSD for multi-chain structure?

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 13 11:29:40 PDT 2014

Hi Oliver,
There isn't a way to do it in one fell swoop, at least not without creating your own attribute assignment file.

The way I would do it, avoiding writing my own scripts, is to repeat the process for each chain.  I.e. for chain A and A' (in the two conformations) I would show one of their sequences (Favorites... Sequence), then associate both structural copies with that same sequence, show the RMSD header, and then use Render by Attribute or the rangecolor command to color by mavRMSD. The process is described in more detail in this previous post:
Repeat the process for chains B and B' etc. making sure to set the same value<->color mapping in the Render tool (or rangecolor command) for each pair.  Or, I guess you could do all the stuff before the coloring for each pair and then just do the coloring of everything at once.  Somewhat tedious but avoids scripting anything or creating your own input file. 

Bear in mind that if you have two only structures, the CA-CA RMSD per residue boils down to simply the CA-CA distance for each pair.  The scripting way would be to measure all of the pairwise CA-CA distances and extrude them in the form of an attribute assignment file to be read in with Define Attribute (to assign the residue attributes), then use Render by Attribute on the resulting attribute for all chains at once.  The assignment file is actually quite a simple text format, but the pain would be measuring all the distances, getting that information from Chimera, and reformatting.

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 Jun 13, 2014, at 11:08 AM, Oliver Clarke wrote:

> Hi all,
> Is there an easy way to color two superimposed structures by RMSD (per C-alpha pair)?
> I had a quick look through the manual and the mailing list and I couldn’t find any easy way to do so for a structure that consists of more than one chain.
> I think this would be a very useful addition to either render by attribute or the calculation of a morph (because presumably the paired CA-CA distances are already calculated in the process of generating the morph).
> I have aligned based on one chain in a complex, and would like to color the entire complex by RMSD (to highlight the parts that move the most between two states of the same complex).
> I can calculate the per CA RMSD using “rmsd #1 #2”, but I can’t see any obvious way to assign that to a residue attribute using the attribute calculator or setattr etc.
> Many thanks,
> Oliver.

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