Dear Tom,
Thank you so much. It looks perfect. and Yes, a layer from our Amyloid.
Best,
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
________________________________ From: Tom Goddard goddard@sonic.net Sent: Tuesday, August 30, 2022 3:49 PM To: Binh Nguyen AnBinh.Nguyen@UTSouthwestern.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Help with Zone features
EXTERNAL MAIL
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
[cid:87179850-7B9F-4EE5-8FD8-9BE5409E5318]
On Aug 30, 2022, at 1:25 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto: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.edumailto: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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