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

[Elaine Meng]

Sorry, no, not after the color zone.  You could change the color of the whole surface before doing the color zone.  Then after color zone, the non-zone parts of the surface will have the color you assigned the whole surface.
Elaine

> On Feb 5, 2019, at 2:36 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> 
> Thank you so much. I do have a follow up question. Is there a way to reverse color the densities that I didn't fit a model/markers in? I mean similar to a reverse selection type strategy to save time.  
> 
> On Fri, Jan 18, 2019 at 12:21 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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. 
> 
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