[Chimera-users] Flattening of coloured icosahedron

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 24 10:59:49 PDT 2015


Hello Roman,
The Flatten Icosahedron tool works on Multiscale Models surfaces for an icosahedral capsid, not on a simple icosahedron surface.  The Multiscale Models surfaces are generated from applying symmetry operations to atomic coordinates of one subunit (for example, command: open viper:1pov)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/flatten/flatten.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>

I don’t know if you or VIPERdb have atomic coordinates for a subunit that would enable you to use Multiscale Models (or even if you do, whether they are in the right orientation and position to coincide with your density map), but if so, you could create the Multiscale Models surfaces, then use Surface Color (in menu under Tools… Volume Data) to color them by the density map values, then use Flatten Icosahedron (in menu under Tools… Higher-Order Structure).

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On Aug 24, 2015, at 6:16 AM, <R.I.Koning at lumc.nl> <R.I.Koning at lumc.nl> wrote:
> 
> Is it possible to flatten a coloured icosahedron surface?
> 
> I have an electron density of a virus, and using shape icosahedron and colour icosahedron surface and surface colour I can colour it according to this density. I would really like to generate a flattened icosahedron (compared to the flatten icosahedron command) from the coloured icosahedron surface. In order to get a 2D map of the colours. Is this possible somehow in Chimera? Is it otherwise possible to export the icosahedron with the coloured surfaces and try in another program (like Maya of Cinema4D?).
> 
> Best regards,
> 
> Roman Koning




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