The annoying workaround for now is to make the atoms/markers transparent before doing the color by zone. E.g. if the atoms or markers are #1, command: transparency #1 50 target a The transparency command default is to only affect surfaces, so “target a” is needed to specify the atoms. If you don’t want the atoms to be transparent, you can change them back to 0% transparent after doing the color by zone. I hope this helps, Elaine
On Jan 5, 2018, at 8:58 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Yashar, I was going to say just use the transparency command, e.g.
transparency #2 50
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>
…but I see that generates an error in the current daily build. I’ll make a ticket to report the bug.
I also tried
volume #2 transparency .5
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general>
…but that did not work after coloring by zone, nor did trying to change the color with a command (ex: volume #2 color pink) or the color well on the Volume Viewer dialog. Another ticket, presumably related to the first.
Sorry for the problems, and thanks for bringing our attention to them. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2018, at 7:30 AM, Yashar Sadian <sadian@embl.de> wrote:
Dear all Is there a command or a way to make a zone colored EM map transparent? -- Best, Yashar Sadian
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