Hi James,
There are a few Chimera commands that let you show a icosahedral cage around a virus PDB model. Basically you use the sym command to make the virus capsid from the PDB asymmetric unit, then use the shape command to make the cage, then optionally use the meshmol command to show the cage with cylinders instead of lines. For example,
open 2bbv
sym #0 surf true
shape icos radius 200 lattice 1,1
meshmol #2 3
color gold #3
There’s also a video showing how to make the cage for an electron microscopy map
Here is the command documentation for more info about sym, shape, meshmol commands:
Tom
On Aug 27, 2015, at 5:11 AM, Geraets, James A
Hi Tom,
A colleague of mine has told me that you have previously made available a script for displaying icosahedrally-symmetric pdb files on an icosahedron net. Would you happen to still have it? I can’t find any sign of it online…
Cheers (and thanks for your continued work on Chimera)
James
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James Geraets
EU Marie Curie Actions Fellow
AIROPico Project
Institute of Biotechnology
PL 56
FI-00014 University of Helsinki
Finland