Hi Binh, Looks like an image of one plane of a an amyloid fibril. Here are example commands that make the attached image. open 6y1a hide ~/A,B style stick color byhet open 10669 from emdb vol zone #2 near /A,B range 3 new true volume #3 color gray transp 0.8 level 4 set bgcolor white graphics silhouette true Tom
On Aug 30, 2022, at 1:25 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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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