[Chimera-users] Icosahedral model

Tom Goddard goddard at sonic.net
Wed Jun 11 08:52:53 PDT 2014


Hi Zhihai,

  You can draw an icosahedron mesh with the Icosahedron Surface tool (menu Tools / Higher-Order Structure), or the Chimera “shape” command, for example,

	shape icosahedron radius 55 orientation 2n5 lattice 2,1

You’ll need to figure out the right radius (just try different values and compare the size to the density map), the density map should be centered (use Volume Viewer menu Features / Coordinates to set the origin for the map), figure out which of the standard icosahedron orientations your map uses (just try different ones and compare to your map), and figure out the two lattice parameters if you want to replicate the protein packing in the capsid.  The graphical Icosahedron Surface tool does not let you set lattice parameters — it only shows a simple 12 vertex icosahedron.

  If you want to turn the mesh into a ball and stick model you use the Chimera “meshmol” command.

  Here is documentation of these commands

	http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#icoscage

	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosahedron.html

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html

  Tom




On Jun 10, 2014, at 8:48 PM, 李智海 <21620101152414 at stu.xmu.edu.cn> wrote:

> Hi,
> I have a density map of an icosahedral capsid, and now i want to make a icosahedral model to represent the capsid. In this model, every corner represent a capsomere. what can i do to display this in Chimera ? Do I require any plug-in?
> Thank you!
> Best wishes!
> 
> Zhihai Li
> 
> School of Life Sciences, Xiamen University.
> Xiang'an Road(South), Xiang'an District, Xiamen City,
> Fujian Province, China.
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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