Generate surface from a model using user defined color
Dear all, I would like to generate surface using my model but I want to keep the color as I defined. My protein contains only one chain so that when I ran Surface command, it generated surface with one color... Is there a way to generate surface to keep my defined color? Super thanks! Hong
Dear Hong, The surface is created as a separate model that gets a chain color, which (as you saw) is generally not the same color as the atoms or ribbons. Chain coloring: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html> You can make the surface the same color as the atoms with command "color fromatoms surfaces" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> ... however, since often when you open a structure there is heteroatom coloring with nitrogens blue, oxygens red, etc. it may have lots of blue and red patches. There is no option to color same as ribbons. So either you can really color all atoms a single color first and then use the "fromatoms" command mentioned above, or just color the surface after you show it, e.g. color tan surfaces color /A dodger blue surfaces (or use "target s" instead of "surfaces" ... means the same thing) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 14, 2022, at 6:43 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear all,
I would like to generate surface using my model but I want to keep the color as I defined. My protein contains only one chain so that when I ran Surface command, it generated surface with one color... Is there a way to generate surface to keep my defined color?
Super thanks! Hong
Hi Hong, If you get tomorrow's (Tuesday Oct 18, 2022) ChimeraX daily build (not the 1.5 release candidate) it will make the surface colors match your cartoon colors. ChimeraX was coloring the molecular surface of chains using a fixed set of colors instead of trying to match the color you set for the atoms of your structure. That seems not so great. So I changed it today so that new molecular surfaces have their color match the ribbon/cartoon color of the residues for that surface. (If the residues have multiple colors then the average is used). Also I added an option to the ChimeraX color command to make the surface colors match the ribbon/cartoon colors. For example color #1 fromcartoons With this command if the residues have different ribbon / cartoon colors then the surface will also have multiple colors matching the residues. Thanks for pointing out the difficulty in getting the surface colors to match the structure colors. Tom
On Oct 14, 2022, at 6:43 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear all,
I would like to generate surface using my model but I want to keep the color as I defined. My protein contains only one chain so that when I ran Surface command, it generated surface with one color... Is there a way to generate surface to keep my defined color?
Super thanks! Hong _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Super thanks Elaine and Tom:) I will wait tomorrow’s built. Hong Sent from my iPhone On Oct 17, 2022, at 7:36 PM, Tom Goddard <goddard@sonic.net> wrote: Hi Hong, If you get tomorrow's (Tuesday Oct 18, 2022) ChimeraX daily build (not the 1.5 release candidate) it will make the surface colors match your cartoon colors. ChimeraX was coloring the molecular surface of chains using a fixed set of colors instead of trying to match the color you set for the atoms of your structure. That seems not so great. So I changed it today so that new molecular surfaces have their color match the ribbon/cartoon color of the residues for that surface. (If the residues have multiple colors then the average is used). Also I added an option to the ChimeraX color command to make the surface colors match the ribbon/cartoon colors. For example color #1 fromcartoons With this command if the residues have different ribbon / cartoon colors then the surface will also have multiple colors matching the residues. Thanks for pointing out the difficulty in getting the surface colors to match the structure colors. Tom [6kmx_surf.png] On Oct 14, 2022, at 6:43 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear all, I would like to generate surface using my model but I want to keep the color as I defined. My protein contains only one chain so that when I ran Surface command, it generated surface with one color... Is there a way to generate surface to keep my defined color? Super thanks! Hong _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
HONG ZHAN -
Tom Goddard