Modifying the transparency of a specific region within a single map
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 zhangnan@nankai.edu.cn
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
Hi Nan, I would suggest the "color zone" command since it appears you have atomic models fit in the map where you want the map to be transparent. As Elaine mentioned color zone will make the parts of the map near the atoms match the color and transparency of the atoms. To avoid changing you atomic model coloring I would open a second copy of your atomic models that you don't display, then color that copy's atoms all gray and transparent, then use color zone with that copy. Here is an example open 1080 from emdb open 1grl fit #2 in #1 To copy the atomic model (can specify multiple models here) combine #2 That made atomic model copy #3, now color and set transparency and use color zone to make map transparent near the atomic model color #3 lightgray transparency 80 color zone #1 near #3 distance 10 hide #3 model Tom
On Jun 7, 2024, at 8:09 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
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participants (3)
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Elaine Meng -
Tom Goddard -
张楠