If I color byhet then color zone a volume, the volume takes some colors from the hetero atom colors. How to reverse byhet coloring? Regards.
Hi Ahmad, As long as your version of ChimeraX is not too old, you can undo the color zone and then undo the color byhet, i.e. use command “undo” twice, or menu: Edit… Undo. Then you can use “color zone” again using whatever coloring you had before the color byhet. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/undo.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 Feb 13, 2020, at 12:18 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
If I color byhet then color zone a volume, the volume takes some colors from the hetero atom colors.
How to reverse byhet coloring?
Regards.
Hi Ahmad, The "color zone" command (color zone #5 near #2 distance 4) only colors parts of the surface within the specified distance range. If part of the surface is beyond the distance from all atoms then it retains its old colors. So if you want those distance regions to be a specific color you should color the whole surface with that color before doing the color zone. Tom
On Feb 13, 2020, at 12:18 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
If I color byhet then color zone a volume, the volume takes some colors from the hetero atom colors.
How to reverse byhet coloring?
Regards. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Ahmad, What I stated in the previous email was not right. When you use "color zone" points on the surface greater than the specified distance from any atom get the surface single color. Multicolored surfaces also remember a single color even when showing the multiple colors and that is the color used for the distant regions. I improved the color zone command just now adding a farColor option that lets you specify the color beyond the distance range. color zone #1 near #2/A distance 4 farColor blue Back to your original question -- the "color zone" command colors a surface to match the atoms. So of course if you use "byhet" coloring on the atoms and then do color zone the surface is going to show the byhet coloring. You need to set the atom colors first to be the colors you want on the surface and then do color zone. Tom
On Feb 13, 2020, at 2:33 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Ahmad,
The "color zone" command (color zone #5 near #2 distance 4) only colors parts of the surface within the specified distance range. If part of the surface is beyond the distance from all atoms then it retains its old colors. So if you want those distance regions to be a specific color you should color the whole surface with that color before doing the color zone.
Tom
On Feb 13, 2020, at 12:18 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
If I color byhet then color zone a volume, the volume takes some colors from the hetero atom colors.
How to reverse byhet coloring?
Regards. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Ahmad Khalifa -
Elaine Meng -
Tom Goddard