[Chimera-users] color key in chimera X

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 18 14:23:24 PDT 2019

Hi Pranav,
ChimeraX does not yet have color-key drawing, sorry.  One possibility for now is that even if you want to make the main image in ChimeraX, you could still make the color key separately in Chimera and then combine them in some image-editing program like Photoshop.

In Chimera, you could use the “colorkey” command as Ibrahim suggests, or the GUI (Tools… Utilities… Color Key).  Either way you would have to define the colors and set values “manually” to match the coloring in ChimeraX, so we understand it is not as convenient as when the image and key are in the same program.

There is also a ChimeraX e-mail list chimerax-users at cgl.ucsf.edu that you can use if you have other issues/questions about ChimeraX specifically.

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

> On Mar 18, 2019, at 12:13 PM, Moustafa, Ibrahim M. <ria2 at psu.edu> wrote:
> Hi Pranav,
>   Not sure about ChimeraX but in Chimera you can use 'colorkey' command line:
> colorkey x1,y1 x2,y2 value1 color1 value2 color2....
> example:
> colorkey 0.1,0.1 0.11,0.5 3.0 blue 4.0 cyan 5.0 green 6.0 yellow 7.0 orange 8.0 red
> You can use the colors and their values from the output of local resolution map.
>  Ibrahim
> From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Pranav Shah <p.shah.lab at gmail.com>
> Sent: Monday, March 18, 2019 2:56 PM
> To: chimera-users at cgl.ucsf.edu BB
> Subject: [Chimera-users] color key in chimera X
> Hi,
> I have a isosurface rendering that I have colored by radius as well as
> local resolution. I want to now place a colour key in the image to
> indicate the relevance of the colors. Is there a way to achieve this
> in ChimeraX? If not, is there a way to easily port the commands to
> Chimera?
> Cheers,
> Pranav
> --
> Pranav Shah
> Postdoctoral Research Fellow.

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