[Chimera-users] Expanding EMdatabank map to full map

Tom Goddard goddard at sonic.net
Mon Mar 3 10:50:42 PST 2014


Hi Jason,

  Yes you can compute the icosahedral full map from an asymmetric unit using the Chimera "vop cover" command.

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover

The tricky part will be to assign the correct center of symmetry and icosahedron orientation for the asymmetric piece using the origin and symmetry options of the volume command

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions

Unfortunately the EMDB usually does not include such symmetry information, and it can be tricky to figure it out when the information is missing.  The vop cover command was intended to extend asymmetric unit maps of crystal unit cells, so you'll need to specify a cellSize argument that is larger than the virus.  Any large size will do so the full map you are computing fits within one crystal unit cell.  You'll also need to specify the rectangular box you want the new map to cover.  Since this was intended for crystal unit cells the command doesn't determine the bounds automatically for point symmetry copies of an asym unit.

  If you tell me which EMDB map I might take a try at getting the right symmetry and box parameters.

	Tom


On Feb 28, 2014, at 7:47 AM, Jason C Porta wrote:

> Greetings, 
>  I am searching for a way to take a map from the EMdatabank which is just a cut-out of an icosahedral asymmetric and generate the full map via the sym operators. I see there are similar options for generating sym-related models, but is there a way to do this for a section of a map in Chimera?
> Many thanks,
> Jason P




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