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