Dear Nan, I can't think of a good way to make just part of a map surface transparent. You may need to make a separate map model for the parts that you want transparent, and make its whole surface transparent. There are "volume zone" and "surface zone" commands that will hide/show parts of the map surface based on distance from atoms, but they do not have an option to keep showing the surface but make it transparent. There is a "color zone" command (or GUI) that will color parts of the map surface to match the colors of nearby atoms, but it does not make the surface transparent (well, you could make the atoms partly transparent, and then use color zone to make the surface color identical to those nearby atoms, and then change the atoms back to their final colors, but that is very indirect and inconvenient). <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacezone.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html> However, you could use "volume splitbyzone" to make separate maps after using "color zone" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#splitbyzone> There is also a "select zone" but it will select the whole map surface, not part of it. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 7, 2024, at 12:57 AM, 张楠 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear developers,
How can I change the transparency of a specific region within a single map, similar to what is shown in the attached image? Is this possible to do in ChimeraX?"
Looking forward to your answer, thank you！
Best regards, Nan