[Chimera-users] Color subunits for map density

[Elaine Meng]

Hi Yangqi,
The choice is really yours, but my guess would be that since you already have an atomic model, you can just color the atomic model atoms how you like, select all those atoms, and then use Color Zone (or “scolor” command “zone” option) to color the nearby map surface to match the atoms. Details:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>

You can also split the map by those colored zones, as mentioned in the Color Zone page.

 (If you used Segment Map then it might not divide up the map exactly the same as your monomers, and it would pick its own coloring, although you could then select and recolor each segment surface.)
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 20, 2018, at 9:56 PM, BuddySphinx <yangqi.gu at yale.edu> wrote:
> 
> Dear Chimera developers,
> I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament?
> Best,
> Yangqi