<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 Jian,<div><br></div><div> Here are the Chimera commands to make the 3iyj map from the asymmetric unit PDB.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>open 3iyj</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>molmap #0 5 sym #0</div><div><br></div><div>and to display it at full resolution and color it radially in the attached images I used the following command</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>volume #0 step 1</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>scolor #0 geom radial cmap rainbow</div><div><br></div><div>The molmap command takes the map id number (#0) then the desired resolution (5 Angstroms), then the symmetry (sym #0) which uses the BIOMT remarks in the PDB file, as described in the molmap command documentation</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a></div><div><br></div><div> Tom</div><div><br></div><div><img height="512" width="512" apple-width="yes" apple-height="yes" apple-inline="yes" id="F9524FC2-9B93-4C77-8597-45F5382AD25B" src="cid:E6F9DC88-D01E-4DDE-9DCB-7D0BD74B2D62@cgl.ucsf.edu"></div><div><br><div><div>On Jun 24, 2014, at 10:21 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Aack! Thanks so much Giovanni, I'm glad you noticed my mistake! <br>Elaine<br><br>On Jun 24, 2014, at 10:17 AM, Giovanni Cardone <<a href="mailto:gcardone@ucsd.edu">gcardone@ucsd.edu</a>> wrote:<br><br><blockquote type="cite">Hi Jian,<br><br>a quick correction to Elain's reply. She mistakenly looked at a different PDB (3iyi instead of 3iyj). 3iyj contains the side chains, so you can follow her initial, exhaustive directions.<br>Incidentally, also in this case the atomic model was derived from a cryo-EM map: however, the two maps deposited (EMDB 5155 and 5156) do not represent all the capsid, but just a portion of it.<br><br>I hope this helps,<br>Giovanni<br><br>On 06/24/2014 09:59 AM, Elaine Meng wrote:<br><blockquote type="cite">Hi Jian,<br>Sorry this is a rather long answer, because I ran into several issues…<br><br>In general, you could<br>(1) build multimer atomic structure of capsid based on symmetry information in the PDB file, using Multiscale Models tool or command "sym" (e.g.: sym #0)<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html</a>><br>(2) simulate density map from atomic structure with command "molmap" (e.g.: molmap # 10) … where 10 is adjustable parameter, see the manual<br><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a>><br><br>However, for 3iyi specifically I see that the atomic structure is only the CA backbone. The process above would still make something that looked like a map, but the "densities" would be nonquantitatively low and you would have to contour at very low level to make it look reasonable.<br><br>From the page for 3iyi at the PDB, I see the structure is from cryoelectron microscopy (cryoEM) in the first place, so I thought it might make more sense just to get the cryoEM map from EMDB, if available.<br><<a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=3iyi">http://www.rcsb.org/pdb/explore/explore.do?structureId=3iyi</a>><br><br>To find out EMDB ID numbers, I looked at the (open access) citation given in that PDB page:<br><br>P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks.<br>Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker TS.<br>Structure. 2010 Mar 10;18(3):390-401<br><<a href="http://www.sciencedirect.com/science/article/pii/S0969212610000328">http://www.sciencedirect.com/science/article/pii/S0969212610000328</a>><br><br>… which gives accession numbers EMD-4159 (for "ExH particles," you would need to read the paper for explanation) and EMD-4150. In Chimera you can fetch EMDB entries with menu: File… Fetch by ID, database: EMDB, or command, e.g.: open emdbID:4159<br><br>Unfortunately, I see that those entries are not found!!! I don't know why. I also could not find them at the EMDB website.<br><br>So, my only idea to get a map is the 2-step process above.<br><br>Or, without making a map, you can show the capsid with each subunit as a "blob" using Multiscale Models (in menu under Tools… Higher-Order Structure). The images at the PDB are similar to that:<br><<a href="http://www.rcsb.org/pdb/explore/images.do?structureId=3IYI">http://www.rcsb.org/pdb/explore/images.do?structureId=3IYI</a>><br><br>I hope this helps,<br>Elaine<br>----------<br>Elaine C. Meng, Ph.D.<br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br>On Jun 24, 2014, at 7:49 AM, "Jian Guan" <<a href="mailto:jug25@psu.edu">jug25@psu.edu</a>> wrote:<br><br><blockquote type="cite">Dear All,<br>I want to make a capsid map from asymmetry unit. The PDB ID is 3iyj, the L1 protein of BPV. The BPV is a T=7, icosahedral capsid. Does anybody know how to make it? Thanks a lot.<br>Sincerely yours,<br>Jian<br></blockquote><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br><br></blockquote><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br><br></blockquote></div><br></div></body></html>