<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Hi Reggie,</div><div><br></div><div> I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div>open 2xyz</div><div>rainbow chain</div><div>sym #0 surf true</div><div><br></div><div># Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation).</div><div><br></div>shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5<div>molmap #0 10 sym i,n25r</div><div><br></div><div><br></div><div><img height="759" width="789" apple-width="yes" apple-height="yes" apple-inline="yes" id="3EC1BE53-5341-4169-B129-D53D1559C77A" src="cid:734A0049-4DEA-4BA1-83F5-40CDCA7434F7"></div><div><br><div><div>On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Tom,<br><br>I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts?<br>I’m currently following directions that are here: <a href="http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html">http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html</a><br><br>All the best,<br>-Reggie<br><br>--<br>Reginald McNulty, Ph.D.<br>Postdoctoral Research Associate<br>The Scripps Research Institute<br>Johnson Lab<br>Department of Integrative Structural and Computational Biology <br>10550, N. Torrey Pines Road, MB-31 <br>La Jolla, California 92037<br><br><br><br><br><br><br></blockquote></div><br></div></body></html>