I don't understand what you want to do. Here is an example of using the hkcage command http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscag... You will want to add a radius option (e.g. radius 330 for 330 Angstrom radius cage) to that example and you will need to figure out the h and k lattice parameters. Chimera cannot figure out the h,k values you need. I usually try a few values by hand and visually determine the correct values. When you say "shape factor" I guess you probably mean "sphere factor", the Chimera term for the radial interpolation factor (0 to 1) between a flat faced icosahedron and a sphere. Chimera has no way to automatically determine that value. I sometimes judge that by eye using the Icosahedron Surface dialog, menu entry Tools / Higher-Order Structure / Icosahedron Surface That dialog has sliders to adjust the radius of the icosahedron and the "sphere factor" so you can interactively try different values. It would be nice if Chimera could automatically determine the icosahedral coordinate system, outer radius, and best sphere factor, but currently that is only done by eye. Tom
Hello,
We are using Chimera to classify viruses. We use pdb files from viper.
We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it?
Thank you.
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