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<p>In my opinion, both of these images look really cool!!!! <br>
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Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Wednesday, November 27, 2019 6:13 PM<br>
<b>To:</b> ChimeraX Users Help<br>
<b>Cc:</b> Christophe Leterrier<br>
<b>Subject:</b> [EXTERNAL] Re: [chimerax-users] ChimeraX stalls when trying to display surfaces from a (strange) group of atoms</font>
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<div>Hi Christophe,
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<div class=""> Using a solvent excluded molecular surface with the surface command with larger probe size as Eric suggested is going to produce a very weird looking surface. These solvent excluded surfaces are made by rolling a ball over the "atoms" so you
get a scalloped appearance. It makes more sense for your data to use a Gaussian surface produced with the molmap command, for example,</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>molmap #1 10 balls true</div>
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<div class="">Attached are images of the Gaussian surface (pink) and the solvent excluded surface (blue). Here are docs on molmap</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimerax_docs_user_commands_molmap.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pxrA27F1CHjJQ19VHMXYPmRhDzgO8n27LN767xP0MP4&s=-DLC9Ypqy51avfavOLQfMdfzanzoEkNJZBhitAuytZM&e=" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html</a></div>
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<div class=""> Tom</div>
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<div class=""><img id="BCA014D3-7FDD-4FA2-8F02-5B990FCED1AA" class="" src="cid:CDC3F2C6-6614-460E-9C38-303E5A8CBB0F@cgl.ucsf.edu"><img id="EE20D170-6E09-4F59-A7BC-58BEDAF0F4C5" class="" src="cid:F857B379-94FB-45D7-97F6-0713B5EE8D80@cgl.ucsf.edu"><br class="">
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<div class="">On Nov 27, 2019, at 2:14 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:</div>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Christophe,
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Because your isolated atoms are spaced much further apart than for an actual molecule, computing a surface with the default parameters (probe radius 1.4Å and grid spacing of 0.5Å takes
a <i class="">very</i> long time and produces a surface that looks like your isolated spheres anyway because the small probe radius doesn’t join any of your “atoms” together. Try this command:</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>surf probe 20 grid 5</div>
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<div class="">You can play around with the actual probe and grid values, just don’t use anything near their default values!</div>
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<div class="">—Eric<br class="">
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<span class="Apple-tab-span" style="white-space:pre"><br class="Apple-interchange-newline">
</span>Eric Pettersen</div>
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<span class="Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
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<div class="">On Nov 27, 2019, at 3:13 AM, Christophe Leterrier <<a href="mailto:christophe.leterrier@univ-amu.fr" class="">christophe.leterrier@univ-amu.fr</a>> wrote:</div>
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<div dir="ltr" class="">Hi,
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<div class="">I'm trying to use ChimeraX to visualize Single-Molecule Localization Microscopy (SMLM) data. In short, the output of an SMLM acquisition and processing is a list of fluorophores XYZ coordinates with associated uncertainty, that can be used to
reconstruct a 3D image.</div>
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<div class="">I have made a script that make a pdb file from these localization so that I can directly display the resulting structure as if it was a protein with a number of random atoms (the only difference is that angstroms in ChimeraX are really nanometers
in my data). <span class="" style="">The rendered pqr file is here (I use a pqr pdb format to specify the radius to the localization uncertainty, hence the variable diameter of each sphere)</span><span class="" style="">:</span></div>
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<div class="" style=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neurocytolab.org_up_Example-5FFile.pqr&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pxrA27F1CHjJQ19VHMXYPmRhDzgO8n27LN767xP0MP4&s=vPnNzyJaX_dbdoerQrjGRREdfg2sDZV1wrKsn1GzhOY&e=" class="">http://www.neurocytolab.org/up/Example_File.pqr</a></div>
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<div class="">The rendering with the "Spheres" view of atoms works well, see a screenshot here:</div>
<div class=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neurocytolab.org_up_Render.png&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pxrA27F1CHjJQ19VHMXYPmRhDzgO8n27LN767xP0MP4&s=CCR-uiiLzR5x6Dv27XtB8qxpLDFI2yDApoPPETG6lzE&e=" class="">http://www.neurocytolab.org/up/Render.png</a></div>
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<div class="">However, when I try to get the enveloppe of the resulting object using the "Surfaces" display (click on Surfaces>Show), ChimeraX hangs (I'm on OSX and get the dreaded infinite rainbow beachball).</div>
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<div class="">Is there a chance that I can get ChimeraX to render the enveloppe object this way, or is it really too far from what it's supposed to do? I can imagine that I'm trying to use ChimeraX for something completely different than its intended use, but
it definitely has a lot of potential for this.</div>
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<div class="">Thank you,</div>
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<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">--<br class="">
Christophe Leterrier<br class="">
NeuroCyto lab<br class="">
INP CNRS UMR 7051<br class="">
Aix Marseille University, France<br class="">
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