[Chimera-users] Icosahedral net from PDB

Tom Goddard goddard at sonic.net
Thu Aug 27 11:11:12 PDT 2015


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

	http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html <http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html>

Here is the command documentation for more info about sym, shape, meshmol commands:

	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html>

  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
> 
> ----------
> 
> James Geraets
> EU Marie Curie Actions Fellow
> AIROPico Project
> 
> Institute of Biotechnology
> PL 56
> FI-00014 University of Helsinki
> Finland

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