[chimera-dev] question: development of a new icosahedral tool to include new lattices relevant for viruses

[Tom Goddard]

Hi Toni,

  Neat!  I wrote the hkcage code and I think adding your 3 additional series t,s,r to that command would be the way for researchers to get the most use out of it.  It could simply be adding one more option to that command that specifies the series.  The code that would be needed is Python that computes the vertex coordinates, a triangulation (a list of 3-tuples of vertex indices), and an edge mask that says which of the triangle edges should be hidden (one integer per triangle with 3-bits 0x1, 0x2, 0x4 indicating if the triangle edge should be shown).  I could incorporate your code into the Chimera and ChimeraX distributions and we would credit you cite your paper in the documentation.  I think it would be quite easy for you to simply modify the cage.py code in your Chimera or ChimeraX distribution, do all the testing, write a bit of documentation describing the new option -- send that to me and I will get it into the daily builds and subsequent releases.

  ChimeraX is the successor of Chimera and ChimeraX 1.0 was just released.  Most researchers are still using Chimera instead of ChimeraX but we expect that to transition over the next few years, so I would suggest making your addition to the ChimeraX code.  But you can make the additions to ChimeraX or Chimera and I can move it to the other if you like, the hkcage code for the two is nearly identical.  ChimeraX uses Python 3 while Chimera uses Python 2.

	https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/hkcage/src/cage.py <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/hkcage/src/cage.py>

	https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/IcosahedralCage/cages.py

  Tom


> On Jun 24, 2020, at 8:49 AM, Antoni Luque Santolaria <aluque at sdsu.edu> wrote:
> 
> Dear Chimera development team,
> 
> My lab is interested in developing (or extending) a new version of the hkcage command in cages.py to include the different icosahedral lattices that have been recently discovered and have important implications for viral structures (see Twarock and Luque, Nature Communications, 2019). We would like to receive advice on what would be the best approach to help integrate the tool to be used and shared with the Chimera community. Would it be better to extend hkcage? Generate a new function? Integrate the function in cages.py? Generate a different python script?
> 
> My lab (https://www.luquelab.com/ <https://www.luquelab.com/>) is part of the Viral Information Institute at San Diego State University (https://viralization.org/ <https://viralization.org/>) and recently discovered, in collaboration with Prof. Reidun Twarock (The University of York), a new set of icosahedral lattices that describe previously uncharacterized viral capsid structures (https://www.nature.com/articles/s41467-019-12367-3 <https://www.nature.com/articles/s41467-019-12367-3>). My lab's goal is to develop a tool in Chimera that reflects these new geometries and helps us analyze viral capsids and other complexes with icosahedral symmetry. We would also like to facilitate the scientific community to use this tool in Chimera. This project will be developed as part of an NSF award.
> 
> Please let us know the best way to proceed.
> 
> Thanks,
> Toni
> 
> 
> -- 
> Antoni Luque, PhD
> http://luquelab.com <http://luquelab.com/>
> Assistant Professor
> Department of Mathematics and Statistics
> Viral Information Institute
> San Diego State University
> 
> Office: GMCS 514
> Phone: 619 594 7244
> email: aluque at sdsu.edu <mailto:aluque at sdsu.edu>_______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev

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