<html><head><meta http-equiv="Content-Type" content="text/html charset=GB2312"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Glad it worked. The command "sym #0 group i,222 surf true¡± will make surfaces for the symmetric copies instead of copying the PDB model 59 times so it will take little memory.<div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br><div><br><div><div>On Jun 24, 2014, at 1:51 PM, Jian Guan wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-US" link="blue" vlink="purple" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="WordSection1" style="page: WordSection1;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 16pt; font-family: 'Times New Roman', serif;">Hi All,<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 16pt; font-family: 'Times New Roman', serif;">It works pretty good. I appreciate it a lot.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 16pt; font-family: 'Times New Roman', serif;">I tried ¡°sym #0 group i,222¡± by myself before your suggestions. It only generate the duplication of PDB map, and it is a heavy job which makes my PC slow. I like your commands.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 16pt; font-family: 'Times New Roman', serif;">Thanks,<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 16pt; font-family: 'Times New Roman', serif;">Have a great day.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 16pt; font-family: 'Times New Roman', serif;">Jian<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">-----Original Message-----<br>From: Elaine Meng<br>Sent: 2014<span lang="ZH-CN" style="font-family: SimSun;">Äê</span>6<span lang="ZH-CN" style="font-family: SimSun;">ÔÂ</span>24<span lang="ZH-CN" style="font-family: SimSun;">ÈÕ</span><span class="Apple-converted-space"> </span>13:21<br>To: Giovanni Cardone<br>Cc: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>; Jian Guan<br>Subject: Re: [Chimera-users] making capsid map from asymmetry unit.</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Aack! Thanks so much Giovanni, I'm glad you noticed my mistake!<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Elaine<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">On Jun 24, 2014, at 10:17 AM, Giovanni Cardone wrote:<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">> Hi Jian,<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">> 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.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">> 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.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">> I hope this helps,<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">> Giovanni<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">> On 06/24/2014 09:59 AM, Elaine Meng wrote:<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Hi Jian,<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Sorry this is a rather long answer, because I ran into several<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> issues¡<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> In general, you could<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> (1) build multimer atomic structure of capsid based on symmetry<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> information in the PDB file, using Multiscale Models tool or command<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> "sym" (e.g.: sym<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> #0)<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html</span></a>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> (2) simulate density map from atomic structure with command "molmap" <o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> (e.g.: molmap # 10) ¡ where 10 is adjustable parameter, see the<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> manual<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> <<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</span></a>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> 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.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> 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.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> <<a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=3iyi" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">http://www.rcsb.org/pdb/explore/explore.do?structureId=3iyi</span></a>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> To find out EMDB ID numbers, I looked at the (open access) citation given in that PDB page:<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker TS.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Structure. 2010 Mar 10;18(3):390-401<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> <<a href="http://www.sciencedirect.com/science/article/pii/S0969212610000328" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">http://www.sciencedirect.com/science/article/pii/S0969212610000328</span></a>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> ¡ which gives accession numbers EMD-4159 (for "ExH particles," you<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> would need to read the paper for explanation) and EMD-4150. In<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Chimera you can fetch EMDB entries with menu: File¡ Fetch by ID,<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> database: EMDB, or command, e.g.: open emdbID:4159<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Unfortunately, I see that those entries are not found!!! I don't know why. I also could not find them at the EMDB website.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> So, my only idea to get a map is the 2-step process above.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> 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:<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> <<a href="http://www.rcsb.org/pdb/explore/images.do?structureId=3IYI" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">http://www.rcsb.org/pdb/explore/images.do?structureId=3IYI</span></a>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> I hope this helps,<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Elaine<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> ----------<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Elaine C. Meng, Ph.D.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> of Pharmaceutical Chemistry University of California, San Francisco<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> On Jun 24, 2014, at 7:49 AM, "Jian Guan" <<a href="mailto:jug25@psu.edu" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">jug25@psu.edu</span></a>> wrote:<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>>> Dear All,<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>>> 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.<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>>> Sincerely yours,<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>>> Jian<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> _______________________________________________<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>> Chimera-users mailing list<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">Chimera-users@cgl.ucsf.edu</span></a><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">>><span class="Apple-converted-space"> </span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</span></a><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">> _______________________________________________<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">> Chimera-users mailing list<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">><span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">Chimera-users@cgl.ucsf.edu</span></a><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">><span class="Apple-converted-space"> </span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline;"><span style="color: windowtext; text-decoration: none;">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</span></a><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">><o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div>_______________________________________________<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</div></blockquote></div><br></div></div></body></html>