<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;">Hi Reggie,<div><br></div><div> You are right that the EMDB 1220 virus capsid has none of the standard icosahedral orientations. It is approximately 3-fold axis along z, and 2-fold axis along x (Chimera orientation 2n3r) but it is maybe 5 degrees off from that. If this capsid was refined with C1 symmetry then there is no reason for it to have a standard orientation. It will be difficult to compute the icosahedral symmetry matrices. I suggest you talk to the author of that map Gabe Lander who has a lab at Scripps, right where you are located.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br><div><br><div><div>On Oct 8, 2014, at 2:07 PM, Reginald McNulty wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Thanks. It works.<div>I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map?</div><div>Reggie<br><div><div>On Oct 8, 2014, at 11:34 AM, Tom Goddard wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div 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><span><2xyz.jpg></span></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></div></blockquote></div><br>
<br></div></div></blockquote></div><br></div></div></body></html>