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

Tom Goddard goddard at sonic.net
Tue Jun 24 10:38:00 PDT 2014

Hi Jian,

  Here are the Chimera commands to make the 3iyj map from the asymmetric unit PDB.

	open 3iyj
	molmap #0 5 sym #0

and to display it at full resolution and color it radially in the attached images I used the following command

	volume #0 step 1
	scolor #0 geom radial cmap rainbow

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



On Jun 24, 2014, at 10:21 AM, Elaine Meng  wrote:

> Aack!  Thanks so much Giovanni, I'm glad you noticed my mistake! 
> Elaine
> On Jun 24, 2014, at 10:17 AM, Giovanni Cardone <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>
>>> (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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