Dear Elaine, Thanks for the instructions. This is what I got, but the map density edge is not as sharp compared to the reference figure (my first email). Is there anything else that I can improve? [cid:c5fc944f-33ff-425a-9454-3c0510e9e67d] Thank you so much, 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: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, August 30, 2022 3:25 PM To: Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Help with Zone features 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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