[chimerax-users] Question about Coulombic scale bar in ChimeraX

[Elaine Meng]

Hi Guipeun,
This is the usual situation: The Color Key is not saying that -10 to +10 are the entire range in your structure, it is just showing how the color changes between -10 and +10.  You would not change the values on the color key unless you also change the coloring.  

Any areas of the surface that have values beyond the range just get the same color as that end of the Color Key. I.e., all surface points with values below -10 (all the way down to the minimum for your surface -13.11) are the pure red shown at one end of the Color Key, and all surface points with values above 10 (up to the maximum for your surface +21) are the pure blue color shown at the other end.  In between -10 and +10 the color gradually changes, and showing that change is the purpose of the Color Key.

The tutorial uses "coulombic" with the default coloring, and the "key true" option in that command shows the values for that default coloring which are red for -10, white for 0, and blue for 10.
<https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#key>

 If you used different value/color settings in the command, then the key would appear with those different settings.

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

P.S. it is recommended to send questions to chimerax-users at cgl.ucsf.edu (CC'd here) unless you are including data that needs to remain private

> On Aug 18, 2022, at 12:14 PM, Guipeun Kang <Guipeun.Kang at UTSouthwestern.edu> wrote:
> 
> Dear Dr. Elaine Meng,
> 
> My name is Guipeun Kang, a postdoctoral researcher in Dr. Ryan Hibbs at UT Southwestern medical center. 
> 
> I have a silly question about scale bar of Coulombic surface. 
> 
> I displayed Coulombic potential of 3eeb, which is an example on ChimeraX tutorial page.  
> https://www.rbvi.ucsf.edu/chimerax/features.html
> 
> In the Log, Coulombic values are minimum -13.11 and maximum 20.86 for chain A, but the scale bar is ranged from -10 to 10 when I add color key as shown in the instructions. 
> https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#key
> 
> My question is:
> When I type command "coulombic protein key true", the range of Coulombic surface of 3eeb is automatically reflected from -10 to 10? Or, should I manually change the scale bar range from -13 to 21 as shown in Log?
> 
> I'm attaching a screenshot of ChimeraX Log and Color Key panel related to my question. 
> 
> I really appreciate your help,
> Guipeun
> 
> <image.png>
> 
> UT Southwestern
> Medical Center
> The future of medicine, today.