[Chimera-users] help on virus visualization

Tom Goddard goddard at sonic.net
Mon Oct 25 10:35:58 PDT 2010

Hi C.J.,

   In addition to what Elaine suggested, you can also mask to an 
icosahedral surface, or a radial interpolation between a flat face 
icosahedron and a sphere.  You would use the Icosahedron Surface dialog 
(menu Tools / Higher-Order Structure) or the "shape" command to make 
this surface and the "mask" command to make a new density map containing 
only the density within the surface.

   All of the Chimera masking techniques just set the density map values 
to zero outside the surface.  This produces a pretty jagged edge between 
density inside and density outside.


> Dear all,
> I want to mask area outside certain surface and to visualize the inner
> capsid of a virus by Chimera.
> Anyone would be kind to help me with that?
> C.J.

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