<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 James,<div class=""><br class=""></div><div class="">&nbsp; There are a few Chimera commands that let you show a icosahedral cage around a virus PDB model. &nbsp;Basically you use the sym command to make the virus capsid from the PDB asymmetric unit, then use the shape command to make the cage, then optionally use the meshmol command to show the cage with cylinders instead of lines. &nbsp;For example,</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre">        </span>open 2bbv</div><div class=""><span class="Apple-tab-span" style="white-space:pre">        </span>sym #0 surf true</div><div class=""><span class="Apple-tab-span" style="white-space:pre">        </span>shape icos radius 200 lattice 1,1</div><div class=""><span class="Apple-tab-span" style="white-space:pre">        </span>meshmol #2 3</div><div class=""><span class="Apple-tab-span" style="white-space:pre">        </span>color gold #3</div><div class=""><br class=""></div><div class="">There’s also a video showing how to make the cage for an electron microscopy map</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre">        </span><a href="http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html" class="">http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html</a></div><div class=""><br class=""></div><div class="">Here is the command documentation for more info about sym, shape, meshmol commands:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre">        </span><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html" class="">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html</a></div><div class=""><br class=""></div><div class="">&nbsp; Tom</div><div class=""><br class=""></div><div class=""><img height="491" width="511" apple-width="yes" apple-height="yes" apple-inline="yes" id="5A8B3EAC-3267-4298-A7AC-D79BCEAE35EF" src="cid:84EB8FF2-E4F1-47BF-8561-A51309D5877B@cgl.ucsf.edu" class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On Aug 27, 2015, at 5:11 AM, Geraets, James A&nbsp;</div><div class="">Hi Tom,<br class=""><br class="">A colleague of mine has told me that you have previously made available a script for displaying icosahedrally-symmetric pdb files on an icosahedron net. Would you happen to still have it? I can’t find any sign of it online…<br class=""><br class="">Cheers (and thanks for your continued work on Chimera)<br class=""><br class="">James<br class=""><br class="">----------<br class=""><br class="">James Geraets<br class="">EU Marie Curie Actions Fellow<br class="">AIROPico Project<br class=""><br class="">Institute of Biotechnology<br class="">PL 56<br class="">FI-00014 University of Helsinki<br class="">Finland<br class=""></div></blockquote></div><br class=""></div></body></html>