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#ico... 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#icoscag...
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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