[Chimera-users] shape factor

Tom Goddard goddard at sonic.net
Thu May 12 09:31:25 PDT 2011

I don't understand what you want to do. Here is an example of using the 
hkcage command


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.


>      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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