[Chimera-users] How to show an icosahedral cage

[Tom Goddard]

Hi Yen-Chywan,

   To show a simple icosahedral cage with 12 triangles use the "shape" 
command.

     shape icos radius 170 orient 222r mesh true divisions 1 color blue 
linewidth 4

Here's documentation

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

   Tom

> 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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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


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