[Chimera-users] Coloring specific amino acid residues in Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 27 09:58:43 PST 2017

Hi MC,
There are a lot of different ways you could go about this.  If you knew what residues they were (e.g. numbers) you could of course specify them directly in a coloring command, or in a selection command and then use the menu for coloring.  Direct specification is a command something like:

color red #1:25.A 

(color model #1 residue 25 in chain A red)

If you don’t know residue numbers or it isn’t that easy to look up, another approach is to align the sequences and then you can easily see which residues are different. You can then select individual positions with the mouse in the sequence alignment, or even select all the positions with differences in a single step.  Details…

PDB IDs for your situation would have been helpful (if any… maybe this is your own new structure), but I tried to find an example with homomultimers: 

(1) open 3fis and 1etx in Chimera

(2) enter command: split
(these are homodimers each with chain A and B, and splitting each chain into its own model is needed to make both chains interact fully with the sequence stuff in the following steps)

(3) choose menu: Tools… Sequence… Align Chain Sequences, choose one chain from 3fis and one from 1etx (doesn’t matter which since they are the same within a structure), OK or Apply to create alignment … in resulting sequence alignment you can see position 74 is different.   In this example only one position is different and you could just select a residue with the mouse in the sequence window to select the corresponding structure residue(s).  However, if there are multiple positions with mutations in one structure relative to the other, the way to select them all at once is with sequence window menu:  Structure… Select by Conservation.  In the resulting dialog, in the top area choose the structure(s) you want to color, in the histogram move the green vertical bars to include 0.5 and not 1, click OK or apply to select those residues.


(4) then you can just use the main menu to color the selected residues, or a color command where “sel” is the specification, e.g.:

color red sel

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

> On Dec 26, 2017, at 11:15 AM, Mariano Carossino <mca259 at g.uky.edu> wrote:
> Hi, 
> I have two trimer structures for the VP7 protein of two different rotavirus strains and I would like to highlight specific amino acid changes between these two. Could you please indicate me how can I color the amino acid residues that differ between these two structures using Chimera?
> Thank you, 
> MC

More information about the Chimera-users mailing list