[Chimera-users] Color subunits for map density

Yangqi Gu yangqi.gu at yale.edu
Wed Dec 12 14:04:02 PST 2018

Hi Elaine,
I tried what you suggested and using the command scolor #0 zone: *.c, now
my c chain density becomes gradient color. Is there anyway showing a single
color, let's say I want it red without gradient. Also, how do I change
multiple chains color at the same time?

On Wed, Nov 21, 2018 at 12:17 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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


Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
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