[chimerax-users] Color by Chemical Shift Perturbations

[Elaine Meng]

Hi Nadun,
Sure, you can put as many value,color pairs in the command as you want.  The example you may be referring to just gives two pairs:

<https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/chemshift.html>

...with command:
color byattribute csp palette 0,lightgray:0.1,green noValueColor skyblue

However, you could just specify more value,color pairs in the palette, for example:

color byattribute csp palette 0,skyblue:0.025,green:0.05,yellow:0.075,orange:0.1,red  noValueColor gray

This is explained in the command help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute>

...specifically the palette options:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options>

You can see lots of color names here, or use command "color list" to show them in the Log.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin>

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

> On Aug 5, 2022, at 11:39 AM, Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi admin,
> I am trying to color the protein surface based on the chemical shift perturbations. As mentioned in the example published on March 15th, 2021, I was able to color the surface. However, I needed to add 6 levels, and I failed to do so. It was possible to define the levels and colors in chimera but I failed to do so in chimerax. Is there a way to solve this?
> Thank you
> 
> Nadun
> 
> Nadun Karunatilleke
> Ph.D. Candidate 
> Dr. James Choy's Lab
> Department of Biochemistry
> Schulich School of Medicine & Dentistry
> Western University
> London, Ontario, Canada N6A 5C1