<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=""><div><blockquote type="cite" class=""><br class="Apple-interchange-newline"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Divjak Maja <<a href="mailto:Maja.Divjak@petermac.org" class="">Maja.Divjak@petermac.org</a>><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Downloading HIV PDB 3j3q?</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">April 1, 2019 at 5:23:39 AM PDT<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class=""></span></div><br class=""><div class=""><div class="">Hi Elaine,<br class=""><br class="">It's me again! Hope you had a nice weekend...<br class=""><br class="">I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here?<br class=""><br class="">Thanks so much for your help, as always,<br class=""><br class="">Maja<br class=""><br class="">Dr Maja Divjak <br class="">BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS)<br class="">Biomedical Animator<br class="">Office of Cancer Research<br class=""><br class=""></div></div></blockquote></div><br class=""><div class="">Hi Maja,<div class="">(forwarding to the address that should be used for for Chimera questions)</div><div class=""><br class=""></div><div class="">It is probably just too big for the memory on your computer to open this structure in Chimera.</div><div class=""><br class=""></div><div class="">Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera. It handles large structures much more efficiently, but it does not have the same set of features as Chimera.</div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimerax/index.html" class="">http://www.rbvi.ucsf.edu/chimerax/index.html</a>></div><div class=""><br class=""></div><div class="">If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. </div><div class=""><<a href="https://www.rcsb.org/structure/3j3q" class="">https://www.rcsb.org/structure/3j3q</a>></div><div class=""><br class=""></div><div class="">Best,</div><div class="">Elaine</div><div class=""><div class="">
-----<br class="">Elaine C. Meng, Ph.D.<br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco
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