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Dear Tom,</div>
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Thank you so much. It looks perfect. and Yes, a layer from our Amyloid.</div>
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Best,</div>
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B</div>
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<span style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt">Binh A. Nguyen, Ph.D.</span></div>
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<span style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt">@ Saelices's Lab</span></div>
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<span style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt">Center for Alzheimer’s and Neurodegenerative Diseases</span><br>
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<span style="margin:0px; font-size:11pt; font-family:Calibri,Helvetica,sans-serif">Peter O’Donnell Jr. Brain Institute</span></p>
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<span style="margin:0px; font-size:11pt; font-family:Calibri,Helvetica,sans-serif">UT Southwestern Medical Center</span></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Tuesday, August 30, 2022 3:49 PM<br>
<b>To:</b> Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Help with Zone features</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">
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<p class="x_MsoNormal" style="line-height:12.0pt; background:#BDD6EE"><span style="font-size:12.0pt; font-weight:bold; color:black">EXTERNAL MAIL</span></p>
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<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><br class="">
</div>
<div> Tom</div>
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<div><img id="x_187219B4-602F-4DED-B75B-482DBDF7E069" width="818" height="514" class="" data-outlook-trace="F:1|T:1" src="cid:87179850-7B9F-4EE5-8FD8-9BE5409E5318"></div>
<div><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="x_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="">
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Manage subscription:<br class="">
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class="">
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