[chimerax-users] Color by Chemical Shift Perturbations

[Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare]

Hi Elaine,
Thanks for the info. It worked.

Best regards

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

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, August 5, 2022 3:17 PM
To: Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare <nkarunat at uwo.ca>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Color by Chemical Shift Perturbations

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

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