[Chimera-users] coloring domains

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 31 09:33:34 PDT 2018

Hi Hui Min,
I don’t know what the SMART output looks like, but I guess it might have residue numbers, or show the domains on the sequence.

If you have residue numbers that go with your structure (pdb file) you can just use them in a “color” command, or “select” command and then use menu: Actions… Color… (etc.) to color the selection. For example, to color residues 35-89 and 112-150 in chain A:

command: color red :35-89.A,112-150.A
- or -
command: select :35-89.A,112-150.A
(then use menu: Actions…Color (etc.))

How to specify residues etc. in commands:

Actions menu:

Actions… Color… all options… allows showing all 60 colors but if you don’t want any of those, you can still define your own by choosing “from editor” in that dialog.

Or, if you want to look at the sequence and choose from there, first open the pdb, then show its sequence (menu: Favorites… Sequence) and then use the mouse to drag a box to select the residues in the sequence window.  Then you can use the Actions menu to color as described above.

There are tutorials for learning these basic actions in Chimera for example: 

… more tutorials can be opened from the Help menu.  Here’s the copy of the same stuff on our website:

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

> On Oct 31, 2018, at 8:00 AM, Hui Min <huim868 at gmail.com> wrote:
> Hi there,
> Sorry to disturb you. I have a question of how to use the Chimera software.
> If I've already got a .pdb file and use SMART to predict the domains, how can 
> I mark the 3D structure with user defined color? Thank you in advance for your help

More information about the Chimera-users mailing list