[Chimera-users] How to show an icosahedral cage

Tom Goddard goddard at sonic.net
Wed May 11 19:10:25 PDT 2011

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.



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


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


We don't distribute it separately.


> 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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