[Chimera-users] Color subunits for map density

[BuddySphinx]

I see. Thank you very much!
Best,
Yangqi

Sent from Mail for Windows 10

From: Elaine Meng
Sent: Wednesday, December 12, 2018 5:41 PM
To: BuddySphinx
Cc: chimera-users
Subject: Re: [Chimera-users] Color subunits for map density

Hi Yangqi,
That is not a gradient.  That is red patches near red-colored atoms (presumably oxygens) and blue patches near blue-colored atoms (presumably nitrogens).  Maybe you don’t know what colors your atoms are if you are only displaying ribbons.  Hide the surface for now, hide ribbons, show atoms,  and color the atoms how you want first, e.g.:

volume #0 hide
~ribbon
display
color sky blue :.C
volume #0 show
scolor #0 zone :.C range 5

(or whatever distance cutoff you want)

Best,
Elaine
 
> On Dec 12, 2018, at 2:30 PM, BuddySphinx <yangqi.gu at yale.edu> wrote:
> 
> Hi Elaine,
> I tried what you suggested. And it looks like this, still gradient.
> <EBB3F6C0EAB24B58B48C5F7760E97009.png>
> I used the command scolor #0 zone :.C range 5
> Best,
> Yangqi
>  
> Sent from Mail for Windows 10
>  
> From: Elaine Meng
> Sent: Wednesday, December 12, 2018 5:26 PM
> To: Yangqi Gu
> Cc: chimera-users
> Subject: Re: [Chimera-users] Color subunits for map density
>  
> Hi Yangqi,
> “scolor” with “zone” option does not use gradients, it just colors the surface to match the specified atoms.  Each patch of surface near some atom becomes the same color as the atom.  So first color the atoms the way you want. 
>  
> Your command looks wrong, so maybe it tried to use gradient coloring instead.  Try something like
>  
> scolor #0 zone  :.C range 5
>  
> where 5 is the distance cutoff, use what you want …or you can specify more than one chain, e.g.
>  
> scolor #0 zone :.C-H range 8
> scolor #0 zone :.C:.F range 8
>  
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>  
> > On Dec 12, 2018, at 2:04 PM, Yangqi Gu <yangqi.gu at yale.edu> wrote:
> >
> > 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?
> > Best,
> > Yangqi
> >
> > 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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>  
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