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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoPlainText><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>Hi All,<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>It works pretty good. I appreciate it a lot.<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:16.0pt;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></p><p class=MsoPlainText><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>Thanks,<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>Have a great day.<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>Jian<o:p></o:p></span></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>-----Original Message-----<br>From: Elaine Meng [mailto:meng@cgl.ucsf.edu] <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> 13:21<br>To: Giovanni Cardone<br>Cc: chimera-users@cgl.ucsf.edu; Jian Guan<br>Subject: Re: [Chimera-users] making capsid map from asymmetry unit.</p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Aack! Thanks so much Giovanni, I'm glad you noticed my mistake! <o:p></o:p></p><p class=MsoPlainText>Elaine<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>On Jun 24, 2014, at 10:17 AM, Giovanni Cardone <<a href="mailto:gcardone@ucsd.edu"><span style='color:windowtext;text-decoration:none'>gcardone@ucsd.edu</span></a>> wrote:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>> Hi Jian,<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> 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></p><p class=MsoPlainText>> 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></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> I hope this helps,<o:p></o:p></p><p class=MsoPlainText>> Giovanni<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> On 06/24/2014 09:59 AM, Elaine Meng wrote:<o:p></o:p></p><p class=MsoPlainText>>> Hi Jian,<o:p></o:p></p><p class=MsoPlainText>>> Sorry this is a rather long answer, because I ran into several <o:p></o:p></p><p class=MsoPlainText>>> issues¡<o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> In general, you could<o:p></o:p></p><p class=MsoPlainText>>> (1) build multimer atomic structure of capsid based on symmetry <o:p></o:p></p><p class=MsoPlainText>>> information in the PDB file, using Multiscale Models tool or command <o:p></o:p></p><p class=MsoPlainText>>> "sym" (e.g.: sym <o:p></o:p></p><p class=MsoPlainText>>> #0)<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html"><span style='color:windowtext;text-decoration:none'>http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html</span></a>><o:p></o:p></p><p class=MsoPlainText>>> (2) simulate density map from atomic structure with command "molmap" <o:p></o:p></p><p class=MsoPlainText>>> (e.g.: molmap # 10) ¡ where 10 is adjustable parameter, see the <o:p></o:p></p><p class=MsoPlainText>>> manual <o:p></o:p></p><p class=MsoPlainText>>> <<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html"><span style='color:windowtext;text-decoration:none'>http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</span></a>><o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> 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></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> 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></p><p class=MsoPlainText>>> <<a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=3iyi"><span style='color:windowtext;text-decoration:none'>http://www.rcsb.org/pdb/explore/explore.do?structureId=3iyi</span></a>><o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> To find out EMDB ID numbers, I looked at the (open access) citation given in that PDB page:<o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks.<o:p></o:p></p><p class=MsoPlainText>>> Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker TS.<o:p></o:p></p><p class=MsoPlainText>>> Structure. 2010 Mar 10;18(3):390-401<o:p></o:p></p><p class=MsoPlainText>>> <<a href="http://www.sciencedirect.com/science/article/pii/S0969212610000328"><span style='color:windowtext;text-decoration:none'>http://www.sciencedirect.com/science/article/pii/S0969212610000328</span></a>><o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> ¡ which gives accession numbers EMD-4159 (for "ExH particles," you <o:p></o:p></p><p class=MsoPlainText>>> would need to read the paper for explanation) and EMD-4150. In <o:p></o:p></p><p class=MsoPlainText>>> Chimera you can fetch EMDB entries with menu: File¡ Fetch by ID, <o:p></o:p></p><p class=MsoPlainText>>> database: EMDB, or command, e.g.: open emdbID:4159<o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> 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></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> So, my only idea to get a map is the 2-step process above.<o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> 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></p><p class=MsoPlainText>>> <<a href="http://www.rcsb.org/pdb/explore/images.do?structureId=3IYI"><span style='color:windowtext;text-decoration:none'>http://www.rcsb.org/pdb/explore/images.do?structureId=3IYI</span></a>><o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> I hope this helps,<o:p></o:p></p><p class=MsoPlainText>>> Elaine<o:p></o:p></p><p class=MsoPlainText>>> ----------<o:p></o:p></p><p class=MsoPlainText>>> Elaine C. Meng, Ph.D.<o:p></o:p></p><p class=MsoPlainText>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department <o:p></o:p></p><p class=MsoPlainText>>> of Pharmaceutical Chemistry University of California, San Francisco<o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> On Jun 24, 2014, at 7:49 AM, "Jian Guan" <<a href="mailto:jug25@psu.edu"><span style='color:windowtext;text-decoration:none'>jug25@psu.edu</span></a>> wrote:<o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>>> Dear All,<o:p></o:p></p><p class=MsoPlainText>>>> 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></p><p class=MsoPlainText>>>> Sincerely yours,<o:p></o:p></p><p class=MsoPlainText>>>> Jian<o:p></o:p></p><p class=MsoPlainText>>> <o:p></o:p></p><p class=MsoPlainText>>> _______________________________________________<o:p></o:p></p><p class=MsoPlainText>>> Chimera-users mailing list<o:p></o:p></p><p class=MsoPlainText>>> <a href="mailto:Chimera-users@cgl.ucsf.edu"><span style='color:windowtext;text-decoration:none'>Chimera-users@cgl.ucsf.edu</span></a><o:p></o:p></p><p class=MsoPlainText>>> <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users"><span style='color:windowtext;text-decoration:none'>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</span></a><o:p></o:p></p><p class=MsoPlainText>> _______________________________________________<o:p></o:p></p><p class=MsoPlainText>> Chimera-users mailing list<o:p></o:p></p><p class=MsoPlainText>> <a href="mailto:Chimera-users@cgl.ucsf.edu"><span style='color:windowtext;text-decoration:none'>Chimera-users@cgl.ucsf.edu</span></a><o:p></o:p></p><p class=MsoPlainText>> <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users"><span style='color:windowtext;text-decoration:none'>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</span></a><o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p></div></body></html>