[Chimera-users] Selecting submodels when they are density maps

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 5 13:57:24 PDT 2012

Hi Javier,
The molmap command has a "modelId" option to specify output map model number:

Thus, you could give the two maps two different model numbers, and then control them separately with the volume command, for example:

molmap #0:.a 7 mod 2
molmap #0:.b 7 mod 3
vol #2 color hotpink
vol #3 color dodgerblue

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 5, 2012, at 1:01 PM, Javier Velazquez wrote:

> Hi,
> I am interested in generating a map from a PDB with 2 chains, and color each chain differently. I can do it very easily using the graphical interface, but I couldn't figure out how to do it from the command line. Here are my commands:
> molmap #0:.A 7
> molmap #0:.B 7
> And now adding color is simple:
> volume #0 color red
> But this adds color to both maps. Is there a way to specify a submap, so I can add color separately. I am looking for something like this:
> volume #0:.A color red
> which I tried and didn't work. Thank you for your help.
> Javier

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