[chimerax-users] radial coloring cryo map

[Elaine Meng]

Hi Ibrahim,
I can't give the exact command because I don't know the center of your system.  The command help is here:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#distance>

So the form of the command could be something like

color radial <surf-model> center <center-spec> coordinateSystem <ref-model>

... where ways to specify the center are:

	• x,y,z (three values separated by commas only) – an arbitrary point, interpreted in scene coordinates unless a different coordinateSystem is given
	• an atom-spec – the center of the bounding box of the specified items
	• cofr – the current center of rotation
	• camera – the viewer position

None of those are the same as center of screen, unless you are using the center-of-rotation method that tracks center of view:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cofr.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Mar 15, 2021, at 9:36 AM, Moustafa, Ibrahim M. <ria2 at psu.edu> wrote:
> 
> Dear all,
> 
>   I am trying to color a cryoem map radially in ChimeraX (to get something similar to surface color by radius in chimera).
> 
> I used the following comand:
> 
> color radial #model 
> 
>  However, the map is colored from one side to the other instead of radial coloring starting from the center. I tried to specify the center of the screen as 0,0,0 but that did not help. 
> 
>     What is the correct command/options to do radial coloring in ChimeraX? 
> 
>   Thanks for help,
>   Ibrahim
> 
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