[Chimera-users] Chimera Plugins

Tom Goddard goddard at sonic.net
Mon Jun 16 17:22:59 PDT 2014


Hi Eric,

  Chimera only as a global subdivision parameter applying to all atoms of all molecules, and the subdivision of the atom spheres will automatically vary based on how many pixels they take on the screen.  So it won’t be possible to control the sphere polyhedron shapes with that parameter.  The Chimera “shape sphere” command has a “divisions” option that controls the subdivision but the finest subdivision is an icosahedron (20 triangles).  You probably want a dodecahedron and octahedron (3 shapes for oxygen, nitrogen, carbon).  This would require Python programming to do in Chimera.  To distinguish the 3d printed atom shapes easily I think the atoms would need to be large, at least 1 cm diameter so you aren’t going to be able to print a protein (it would be huge), only small molecules with ten to a hundred atoms would be feasible.  Chimera is mostly oriented to proteins and larger molecular structures with thousands of atoms or more.  Your previous question about printing crystal lattices was also more of interest for small molecules again not the focus area of Chimera.  That said, if you are willing to program Chimera Python scripts these things can be done.

	Tom



On Jun 16, 2014, at 3:12 PM, Eric Bell wrote:

> Hello,
> 
> Does a list exist somewhere of plugins developed for Chimera, or would we need to find them posted separately on a host site?
> 
> Also, I found recently a software that gives preset .stl mesh resolutions for all atoms of the same element so that when they are 3d-printed, the atoms can all be distinguished from one another: http://cad4.cpac.washington.edu/WinXMorphHome/Cif2VRMLHome/Cif2VRML.htm
> However, the rest of the software seems lacking in reference to chimera's capabilities, is there any way that Chimera could have a similar feature?  Ideally it would allow the "subdivisions" property of the viewing effects apply to every element, similar to how radius applies to all atoms of the same element.
> 
> Thanks,
> Eric
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