<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi George,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>First, that script measures the radius of gyration for all the atoms in a model, not just ligands atoms or some subset of the model’s atoms. So, my best guess is that the model that’s from your MD simulation has a lot solvent atoms that Chimera isn’t displaying by default. So you should check that there are the same number of atoms in both models. One way to do that is with the command:</div><div class=""><br class=""></div><div class="">sel #0 (number of selected atoms [all of model 0] shown in the status line)</div><div class="">sel #1 (same thing for model 1).</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>If the difference in the models is the solvent you would want to use the command “delete solvent” before running the gyration script.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Apr 6, 2017, at 12:35 PM, George Tzotzos <<a href="mailto:gtzotzos@me.com" class="">gtzotzos@me.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Taking a reference PDBID 3n7h, I’ve generated for an MD simulation topology and restart files.<br class=""><br class="">I’ve loaded on Chimera 3n7h and then the starting frame of the MD simulation. <br class="">Used the MatchMaker and found perfect superposition of the protein backbone and two ligands (3n7h is #0 and the ligands #0:129.A and #0.132.B<br class=""><br class="">I run the radius of gyration script (see attached). I found that the radii of gyration for the ligands in the two models are completely different.<br class=""><br class="">#0 center of mass: 12.6543 10.4356 15.4086, radius of gyration: 21.182<br class="">#1 center of mass: 42.7381 42.5171 42.6163, radius of gyration: 37.390<br class=""><br class="">I don’t follow why this is so. Any explanation would be most welcome.<br class=""><br class="">A second question regards the units of the radii of gyration. Are they Angstrom or nm?<br class=""><br class="">Thank you in advance<br class=""><br class="">George<br class=""><br class=""><span id="cid:3031B1F7-BED3-4B17-A4B8-80A94577961C@cgl.ucsf.edu"><rad_gyration.py></span>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>