Oops, I accidentally sent help links to my own "preview" documentation. The official links are instead: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style>
On Dec 4, 2023, at 10:25 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, Do you need only part of the surface transparent? I did have the same problem with only part of the surface transparent, e.g.
open 1plx coordset true surf transp :tyr 80 coordset #1
... but when I make the whole surface transparent, it works for all of the trajectory frames, e.g.
open 1plx coordset true surf transp 80 coordset #1
Another possibility is to show the surface as mesh, but that also applies to the whole surface:
surface style mesh
<https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/surface.html...>
About how to make the surface calculation simpler, you could use a bigger "gridSpacing" value with the "surface" command, e.g.:
surf grid 2
<https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/surface.html>
Alternatively, you could use "resolution" with the "surface" command but by default that would make a Gaussian surface that does not retain association with individual atoms, so again you wouldn't be able to specify only certain residues as transparent because the surface wouldn't "know" which parts go with which atoms. See surface help link above for details.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2023, at 3:32 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am working on molecular visualization of membrane system from the md trajectory loaded in the Chimera-x using the open coordset true command.
The issue is with the surface representation of the membrane: transparency :OL,PA,PE,PC 80 target s which are applied only on the current frame (not on the whole trajectory).
Also when I try to make a movie of the system the presence of the surface does slow down everything. Which options could be useful e.g. to decrease the quality of the surface representation ?
Many thanks in advance
Enrico
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