EXTERNAL MAIL
Dear Binh,
It looks more like an electron density map (not solvent-accessible surface). So you would need to open an atomic structure and open its electron density map, and show the structure as sticks and the map as a mesh. For example commands, see the Quick Start
Guide, scroll down to the next-to-the last section that shows 1a0m and its density map. This includes a "vol zone" command.
<
https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html>
Or if you are using the GUI interactively you can adjust the map style (e.g. mesh or not) and level using the Volume Viewer tool, which automatically appears when you open a density map file.
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>
If you want a similar thing but only with molecular surface, not density map, then you don't need zone. You can just show the surface for whatever parts you want by specifying in a command or selecting. E.g.
open 1gcn
hide ribbons
show atoms
surface :1-8
surface style mesh
...or you could make surface transparent...
transparency 50
surface style solid
Details of all of the commands are in the help:
<
https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX developers,
>
> Would you please show me how to make this following figure?
> <image.png>
>
> I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it.
> Any hint is much appreciated.
>
> Warm regards,
>
> B
>
>
> _____________________________________________
> Binh A. Nguyen, Ph.D.
> @ Saelices's Lab
> Center for Alzheimer’s and Neurodegenerative Diseases
> Peter O’Donnell Jr. Brain Institute
> UT Southwestern Medical Center
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