[Chimera-users] making capsid map from asymmetry unit.

[Jian Guan]

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.

Thanks,

Have a great day.

Jian

 

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
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! 

Elaine

 

On Jun 24, 2014, at 10:17 AM, Giovanni Cardone < <mailto:gcardone at ucsd.edu>
gcardone at ucsd.edu> 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>
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>
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>
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>
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>
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" < <mailto:jug25 at psu.edu>
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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