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

[Elaine Meng]

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.
Elaine

> 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.