[Chimera-users] How to color density maps using markers?

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 18 09:21:46 PST 2019

Hi Ahmad,
I believe you have to do it in one step.  Color all the atomic models, select all the atomic models at the same time, then do the coloring with Color Zone.

> On Jan 17, 2019, at 11:43 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> Thanks. When I try to color a different part of the map, it removes the first color. How can I save the colors to the map? P.s. I use atomic models for the coloring. 
> On Thu, Jan 17, 2019 at 5:05 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ahmad,
> There’s not really that many steps to it.  You just need to select the markers and then use the Color Zone tool.  There is a little more description here
> <http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#colorzone>
> ...and in the Color Zone manual page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
> As mentioned in that page, you can also do it with the “scolor” command “zone” option.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jan 17, 2019, at 9:19 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> > 
> > I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it. 
> > 
> > Best regards. 

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