[Chimera-users] How to show an icosahedral cage

[Tom Goddard]

Hi Yen-Chywan,

   The Chimera "hkcage" command makes a cage of pentagons and hexagons 
to show virus symmetry.  For example,

     open emdbID:1058
     hkcage 1 1 radius 170 orient 222r linewidth 4 color blue

The hkcage command has options for the lattice parameters for your 
virus, its radius, what icosahedral coordinate system is being used.  
Here's the documentation.

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

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

The meshmol command can make the edges of the cage cylinders instead of 
lines.

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

The HHMI virus viewer Chimera tool is not part of the standard Chimera 
distribution.  It was made for a CD distributed by the Howard Hughes 
Medical Institute

     http://wwwtest.cgl.ucsf.edu/Outreach/ViralOutbreak/index.html
     http://www.hhmi.org/catalog/main?action=product&itemId=366

We don't distribute it separately.

    Tom

> Dear Tom,
>
> I attend Scripps cryoEM workshop before and meet you there.
>
> Attach please find a screen capture of a virus. But there is a 
> icosahedra cage. My question is how to display that cage with my virus 
> volume?
>
> I did find it in HHMI virus viewer demo movie. But where can download 
> this viewer?
>
> Thanks
>
> Yen-Chywan
>


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