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

Tue Jun 24 10:46:13 PDT 2014

Hi Jian,

  To make the image from my previous image look pretty I also enabled shadows “set shadow”, set the background white “set bgcolor white”, and turned on silhouette edges “set silhouette”.  The shadows help give depth to the image by making the canyons on the surface darker, and the silhouette edges add black lines that also improve the appearance of depth.  The silhouette edges slow down the rendering a lot though (5 times slower), so I only use that for saving images.

	Tom

On Jun 24, 2014, at 10:38 AM, Tom Goddard <goddard at sonic.net> wrote:

> 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
> 
> 	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html
> 
>   Tom
> 
> <3iyj_molmap.jpg>
> 
> 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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