How to set RGB color for user selected atoms?
Hi
How do i set RGB colors for user-selected atoms? Or for custom atom selections? Cmd line?
Regards
-D
Donovan Chin | Director of Computational Drug Discovery | +1 617 899 5333 | dchin@arrakistx.commailto:dchin@arrakistx.com
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Hi Donovan, If you prefer the menu, the way to use custom colors for the selected atoms is "Actions... Color... From Editor". That will open the system-specific color editor dialog for choosing a color interactively (i.e., the Mac one is a bit different from Windows, etc.). Generally all of them allow specifying the color in various ways including as RGB components.
Simply using "Actions... Color... From Editor" wil color not just the atoms, but their ribbons, molecular surfaces, etc. If you want to color only specific representations, choose "Actions... Color... All Options" which will open a Color Actions dialog with such choices. That dialog also has a "From Editor" button to specify the color interactively. http://rbvi.ucsf.edu/chimerax/docs/user/tools/coloractions.html
If you prefer commands, you can specify selected atoms directly in the command as "sel" or if it is a named custom selection, by whatever name you gave it. The color itself can be given as R,G,B components on the 1-100 scale, e.g. for red
color sel 100,0,0 target a
The "target a" in that example limits coloring to the atoms specifically, or you can omit it to color all representations of the atoms (atoms, ribbons, molecular surface patches of the selected atoms).
If using commands, you don't have to go through selections at all. You could just specify the atoms directly, e.g.
color ligand yellow color #4/A:25 purple target r
Color command: http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple
Command-line specification of atoms, residues, etc. http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
There are several other ways to specify colors, including by components, or as hex codes, or using built-in or custom names: http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2020, at 12:47 PM, Donovan Chin DChin@arrakistx.com wrote:
Hi How do i set RGB colors for user-selected atoms? Or for custom atom selections? Cmd line? Regards -D
Donovan Chin | Director of Computational Drug Discovery | +1 617 899 5333 | dchin@arrakistx.com
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