[chimerax-users] Help with Zone features

[Elaine Meng]

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 at 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