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

[Antoni Luque Santolaria]

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/) is part of the Viral Information
Institute at San Diego State University (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). 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
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
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