transparency around the model only
Dear colleagues,
I have a cryo-EM 3D map and model.
A model is fitted for only part of my cryo-EM map.
Is there a command to make the map transparent only where the model is fitted in?
Thank you.
Kind regards, Dmitry
Hi Dmitry, The only way I can think of is somewhat stupid, i.e., more trouble than it should be:
(1) make the atomic structure the transparent color that you actually want for that part of the surface (2) use color zone to make the surface near the atomic structure match the atomic structure (which includes its transparency) (3) then change the atomic structure to the nontransparent color(s) that you really want it to have
For example, if I have atomic structure #1 fitted into map surface #2 and I want the surface within 6 Angstroms of the atoms to be transparent cyan:
color #1 cyan transparency 50 color zone #2 near #1 distance 6 color #1 tan transparency 0
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
At first I thought I could use "select zone" instead and then just do the coloring of the nearby surface directly rather than via the atomic structure, but that seems to select the entire isosurface if any of it is within the zone. https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone
Another related command "surface zone" just does hide/show rather than coloring. https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 Jan 31, 2024, at 2:19 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues,
I have a cryo-EM 3D map and model.
A model is fitted for only part of my cryo-EM map.
Is there a command to make the map transparent only where the model is fitted in?
Thank you.
Kind regards, Dmitry
There is no way to select a patch (ie subset of triangles) of a non-molecular surface. So Elaine's suggestion of the distance-based color zone is the way to do this.
Tom
On Jan 31, 2024, at 8:54 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dmitry, The only way I can think of is somewhat stupid, i.e., more trouble than it should be:
(1) make the atomic structure the transparent color that you actually want for that part of the surface (2) use color zone to make the surface near the atomic structure match the atomic structure (which includes its transparency) (3) then change the atomic structure to the nontransparent color(s) that you really want it to have
For example, if I have atomic structure #1 fitted into map surface #2 and I want the surface within 6 Angstroms of the atoms to be transparent cyan:
color #1 cyan transparency 50 color zone #2 near #1 distance 6 color #1 tan transparency 0
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
At first I thought I could use "select zone" instead and then just do the coloring of the nearby surface directly rather than via the atomic structure, but that seems to select the entire isosurface if any of it is within the zone. https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone
Another related command "surface zone" just does hide/show rather than coloring. https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 Jan 31, 2024, at 2:19 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues,
I have a cryo-EM 3D map and model.
A model is fitted for only part of my cryo-EM map.
Is there a command to make the map transparent only where the model is fitted in?
Thank you.
Kind regards, Dmitry
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participants (3)
-
Dmitry Semchonok -
Elaine Meng -
Tom Goddard