<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="">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://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html" 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=""><img apple-inline="yes" id="BCA014D3-7FDD-4FA2-8F02-5B990FCED1AA" src="cid:CDC3F2C6-6614-460E-9C38-303E5A8CBB0F@cgl.ucsf.edu" class=""><img apple-inline="yes" id="EE20D170-6E09-4F59-A7BC-58BEDAF0F4C5" src="cid:F857B379-94FB-45D7-97F6-0713B5EE8D80@cgl.ucsf.edu" class=""><br class=""><div><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=""><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="">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><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 style="caret-color: rgb(0, 0, 0); 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;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); 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;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); 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;" class=""><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 style="" 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 style="" class="">:</span></div><div class=""><div style="" class=""><a href="http://www.neurocytolab.org/up/Example_File.pqr" 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="http://www.neurocytolab.org/up/Render.png" 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>
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