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.edu<mailto: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<mailto: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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today.
