Color by Chemical Shift Perturbations
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
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@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
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@cgl.ucsf.edu> Sent: Friday, August 5, 2022 3:17 PM To: Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare <nkarunat@uwo.ca> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@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@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
participants (2)
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Elaine Meng -
Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare