<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">It looks like the example image Binh provided also used either `lighting flat` or `lighting soft`. At least I get something a bit closer to the example image when I rerun Tom’s example and add either of these lighting commands.<div class="">Cheers,<br class=""><div class=""><div class=""><div class=""><div class=""><br class=""></div><div class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div>Guillaume</div><div><br class=""></div></div></div></div>
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<div><br class=""><blockquote type="cite" class=""><div class="">On 30 Aug 2022, at 22:49, Tom Goddard via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Binh,</div><div class=""><br class=""></div><div class=""> Looks like an image of one plane of a an amyloid fibril. Here are example commands that make the attached image.</div><div class=""><br class=""></div><div class="">open 6y1a</div><div class="">hide ~/A,B</div><div class="">style stick</div><div class="">color byhet</div><div class="">open 10669 from emdb</div><div class="">vol zone #2 near /A,B range 3 new true</div><div class="">volume #3 color gray transp 0.8 level 4</div><div class="">set bgcolor white</div><div class="">graphics silhouette true</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><span id="cid:87179850-7B9F-4EE5-8FD8-9BE5409E5318"><6y1a.png></span></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Aug 30, 2022, at 1:25 PM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Binh,<br class="">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.<br class=""><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html" class="">https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html</a>><br class=""><br class="">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.<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html</a>><br class=""><br class="">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.<br class=""><br class="">open 1gcn<br class="">hide ribbons<br class="">show atoms<br class="">surface :1-8<br class="">surface style mesh<br class=""><br class="">...or you could make surface transparent...<br class=""><br class="">transparency 50<br class="">surface style solid<br class=""><br class="">Details of all of the commands are in the help:<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands" class="">https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><blockquote type="cite" class="">On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Dear ChimeraX developers,<br class=""><br class="">Would you please show me how to make this following figure?<br class=""> <image.png><br class=""><br class="">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. <br class="">Any hint is much appreciated.<br class=""><br class="">Warm regards,<br class=""><br class="">B<br class=""><br class=""><br class="">_____________________________________________<br class="">Binh A. Nguyen, Ph.D.<br class="">@ Saelices's Lab<br class="">Center for Alzheimer’s and Neurodegenerative Diseases<br class="">Peter O’Donnell Jr. Brain Institute<br class="">UT Southwestern Medical Center<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></div></blockquote></div><br class=""></div></div></div></div></body></html>