Re: [chimerax-users] [Chimera-users] Chimera X color by attribute middle range value
Hi Marcell! In ChimeraX, you can control which colors go with which values in the "palette" option of the "color byattribute" command. This option can take color/value pairs, and the "range" option is not needed in your situation (if I understand correctly). As you found, if you only give the range, it will spread out the colors evenly.
Here's an example of value,color pairs if you want to color by attribute named "blah" using dodger blue for 0.2, red for 1.0, and gold for 4.0:
color byattr blah palette 0.2,dodgerblue:1.0,red:4.0,gold
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
There are lots of named colors, although you could use hex codes instead if the named ones aren't quite what you want. https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html
ChimeraX does not yet have a color-by-attribute GUI although that is something we would like to have eventually. The Color Key tool is just for drawing a color key to explain the coloring, but does not itself affect the structure coloring.
By the way, you may be interested in the chimerax-users@cgl.ucsf.edu mailing list (CC'd on this reply) for questions/discussion specifically about ChimeraX.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 11, 2022, at 5:07 PM, Zimanyi, Marcell via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello Chimera Community,
I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera, I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't see a way to update the coloring on the residues themselves.
Could you please help me figure out how to set attribute range with 3 values as in Chimera?
Thanks, Marcell
Hi Elaine,
Thank you so much, this is exactly what I was looking for; I have residues colored the way I like now. I appreciate your answer, and I will be sure to join the ChimeraX mailing list as well.
Best wishes,
Marcell ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, April 11, 2022 5:34 PM To: Zimanyi, Marcell Marcell.Zimanyi@ucsf.edu Cc: chimera-users@cgl.ucsf.edu chimera-users@cgl.ucsf.edu; ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Chimera X color by attribute middle range value
Hi Marcell! In ChimeraX, you can control which colors go with which values in the "palette" option of the "color byattribute" command. This option can take color/value pairs, and the "range" option is not needed in your situation (if I understand correctly). As you found, if you only give the range, it will spread out the colors evenly.
Here's an example of value,color pairs if you want to color by attribute named "blah" using dodger blue for 0.2, red for 1.0, and gold for 4.0:
color byattr blah palette 0.2,dodgerblue:1.0,red:4.0,gold
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
There are lots of named colors, although you could use hex codes instead if the named ones aren't quite what you want. https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html
ChimeraX does not yet have a color-by-attribute GUI although that is something we would like to have eventually. The Color Key tool is just for drawing a color key to explain the coloring, but does not itself affect the structure coloring.
By the way, you may be interested in the chimerax-users@cgl.ucsf.edu mailing list (CC'd on this reply) for questions/discussion specifically about ChimeraX.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 11, 2022, at 5:07 PM, Zimanyi, Marcell via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello Chimera Community,
I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera, I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't see a way to update the coloring on the residues themselves.
Could you please help me figure out how to set attribute range with 3 values as in Chimera?
Thanks, Marcell
participants (2)
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Elaine Meng -
Zimanyi, Marcell