[Chimera-users] making capsid map from asymmetry unit.
goddard at sonic.net
Tue Jun 24 13:59:13 PDT 2014
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.
On Jun 24, 2014, at 1:51 PM, Jian Guan wrote:
> Hi All,
> It works pretty good. I appreciate it a lot.
> 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.
> Have a great day.
> -----Original Message-----
> From: Elaine Meng
> Sent: 2014年6月24日 13:21
> To: Giovanni Cardone
> Cc: chimera-users at cgl.ucsf.edu; Jian Guan
> Subject: Re: [Chimera-users] making capsid map from asymmetry unit.
> Aack! Thanks so much Giovanni, I'm glad you noticed my mistake!
> On Jun 24, 2014, at 10:17 AM, Giovanni Cardone wrote:
> > Hi Jian,
> > 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.
> > 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.
> > I hope this helps,
> > Giovanni
> > On 06/24/2014 09:59 AM, Elaine Meng wrote:
> >> Hi Jian,
> >> Sorry this is a rather long answer, because I ran into several
> >> issues…
> >> In general, you could
> >> (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)<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
> >> (2) simulate density map from atomic structure with command "molmap"
> >> (e.g.: molmap # 10) … where 10 is adjustable parameter, see the
> >> manual
> >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
> >> 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.
> >> 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.
> >> <http://www.rcsb.org/pdb/explore/explore.do?structureId=3iyi>
> >> To find out EMDB ID numbers, I looked at the (open access) citation given in that PDB page:
> >> P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks.
> >> Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker TS.
> >> Structure. 2010 Mar 10;18(3):390-401
> >> <http://www.sciencedirect.com/science/article/pii/S0969212610000328>
> >> … 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
> >> Unfortunately, I see that those entries are not found!!! I don't know why. I also could not find them at the EMDB website.
> >> So, my only idea to get a map is the 2-step process above.
> >> 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:
> >> <http://www.rcsb.org/pdb/explore/images.do?structureId=3IYI>
> >> I hope this helps,
> >> Elaine
> >> ----------
> >> Elaine C. Meng, Ph.D.
> >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department
> >> of Pharmaceutical Chemistry University of California, San Francisco
> >> On Jun 24, 2014, at 7:49 AM, "Jian Guan" <jug25 at psu.edu> wrote:
> >>> Dear All,
> >>> 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.
> >>> Sincerely yours,
> >>> Jian
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