Dear Tom,

 

If you look at the attach figure carefully, you will find it is not hkcage. In the figure it connect all the 5 fold vertex. How can we generate it?

 

Yen-Chywan

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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