<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="">Reminds me of a lava lamp. :-)<div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 27, 2019, at 3:19 PM, Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu" class="">rkhayat@ccny.cuny.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class="">In my opinion, both of these images look really cool!!!! <br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div id="Signature" style="caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><div name="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; margin: 0px;" class="">Reza Khayat, PhD<div class="">Assistant Professor </div><div class="">City College of New York</div><div class="">Department of Chemistry</div><div class="">New York, NY 10031</div></div></div><div style="caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; 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; background-color: rgb(255, 255, 255); text-decoration: none; word-wrap: break-word; line-break: after-white-space;" class=""><hr tabindex="-1" style="display: inline-block; width: 505.671875px;" class=""><div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" class="">chimerax-users-bounces@cgl.ucsf.edu</a>> on behalf of Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, November 27, 2019 6:13 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>ChimeraX Users Help<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>Christophe Leterrier<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] Re: [chimerax-users] ChimeraX stalls when trying to display surfaces from a (strange) group of atoms</font><div class=""> </div></div><div class="">Hi Christophe,<div class=""><br class=""></div><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><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>molmap #1 10 balls true</div><div class=""><br class=""></div><div class="">Attached are images of the Gaussian surface (pink) and the solvent excluded surface (blue). Here are docs on molmap</div><div class=""><br class=""></div><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><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><span id="cid:CDC3F2C6-6614-460E-9C38-303E5A8CBB0F@cgl.ucsf.edu"><image1.png></span><span id="cid:F857B379-94FB-45D7-97F6-0713B5EE8D80@cgl.ucsf.edu"><image2.png></span><br class=""><div class=""><br class=""><blockquote type="cite" class=""><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><br class="Apple-interchange-newline"><div class=""><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<span class="Apple-converted-space"> </span><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><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>surf probe 20 grid 5</div><div class=""><br class=""></div><div class="">You can play around with the actual probe and grid values, just don’t use anything near their default values!</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class=""><div class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline">
</span>Eric Pettersen</div><div class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><span class="Apple-tab-span" style="white-space: pre;"></span>UCSF Computer Graphics Lab</div><div class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><br class=""></div></div><div class=""><br class=""><blockquote type="cite" class=""><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><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Hi,<div class=""><br class=""></div><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><div class=""><br class=""></div><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="Apple-converted-space"> </span><span class="">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="">:</span></div><div class=""><div class=""><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></div><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><div class=""><br class=""></div><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><div class=""><br class=""></div><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><div class=""><br class=""></div><div class="">Thank you,</div><div class=""><br class=""></div><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=""></div><br class=""></div></div><div class=""><br class=""></div></div></div></div></div></div></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=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pxrA27F1CHjJQ19VHMXYPmRhDzgO8n27LN767xP0MP4&s=OSdC41yEX73xCXgqTAwDUs-Hl9ghFF7kQGa30Yu4qec&e=" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></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=""><a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></div><span style="caret-color: rgb(0, 0, 0); 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