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Dear Elaine,</div>
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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?</div>
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<img style="max-width:100%" class="w-284 h-190" size="102293" contenttype="image/png" data-outlook-trace="F:1|T:1" src="cid:c5fc944f-33ff-425a-9454-3c0510e9e67d"><br>
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Thank you so much,</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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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, August 30, 2022 3:25 PM<br>
<b>To:</b> Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Help with Zone features</font>
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<div class="PlainText">EXTERNAL MAIL<br>
<br>
Dear Binh,<br>
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>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html">https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html</a>><br>
<br>
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>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html">https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html</a>><br>
<br>
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>
<br>
open 1gcn<br>
hide ribbons<br>
show atoms<br>
surface :1-8<br>
surface style mesh<br>
<br>
...or you could make surface transparent...<br>
<br>
transparency 50<br>
surface style solid<br>
<br>
Details of all of the commands are in the help:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands">https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
><br>
> Dear ChimeraX developers,<br>
><br>
> Would you please show me how to make this following figure?<br>
> <image.png><br>
><br>
> 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>
> Any hint is much appreciated.<br>
><br>
> Warm regards,<br>
><br>
> B<br>
><br>
><br>
> _____________________________________________<br>
> Binh A. Nguyen, Ph.D.<br>
> @ Saelices's Lab<br>
> Center for Alzheimer’s and Neurodegenerative Diseases<br>
> Peter O’Donnell Jr. Brain Institute<br>
> UT Southwestern Medical Center<br>
<br>
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.<br>
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