[chimerax-users] Volumes

[Tom Goddard]

Tony is right.  And the Surface Color user interface panel from Chimera has not been implemented in ChimeraX so you have to use the "color sample" command.  I may add the Surface Color user interface panel in the next week or two since I am working on adding missing volume data user interfaces in ChimeraX right now.

	Tom


> On Mar 9, 2021, at 10:43 AM, Anthony James Schaefer <tony.schaefer at uga.edu> wrote:
> 
> Colton,
> 
> I think you're looking for the sample and map keywords of the color​ command. I'm not sure if there's a tool for doing this like the Surface Color tool in Chimera. 
> 
> https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sample <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sample>
> 
> For example, I've got an electron isodensity surface in model #1 and the ESP in model #2. I can color the electron density based on the ESP with
> 
> `color sample #1 map #2 palette -0.024,red:-0.012,yellow:0,green:0.012,cyan:0.024,blue` 
> 
> This will color #1 rainbow colors based on the ESP values between -0.024 to 0.024 from #2. The custom palette specification is the thresholds levels and colors separated by commas, with each of those separated by colons.
> 
> https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette> 
> 
> I used color names, but there are several other ways to specify colors:
> 
> https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>
> 
> 
> Best,
> 
> Tony
> From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu <mailto:chimerax-users-bounces at cgl.ucsf.edu>> on behalf of Colton Carlson <cdc01 at chem.ubc.ca <mailto:cdc01 at chem.ubc.ca>>
> Sent: Tuesday, March 9, 2021 12:39 PM
> To: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: [chimerax-users] Volumes
>  
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
> 
> 
> Hello,
> 
> I am just wondering if ChimeraX has added the ability to colour surfaces based on the values of a different surface? That is, input 2 cube files, then colour one cube file based on the values of the other. It is available in the other version of chimera, but the only information I could find on this was from 2018 and said it was not yet implemented in ChimeraX.
> 
> Thanks a bunch!
> Colton
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