capsid-generator

This repository contains the codes and instructions to generate and visualize the capsid models to investigate icosahedral capsids with 3-fold centered hexamers or all skewed/split hexamers.

Description of each element in the repository:

• T-number_generator.py: This Python script generates the sequence of T-number capsids up to a certain maximum T-number specified by the user (Tmax parameter). The script generates a tsv data file (T-number_capsids_squences.tsv).
• T_H.py: Script that contains a function to determine icosahedral capsids that contain a centered hexamer on a global 3-fold axis.
• T-number_hexamer_symmetries_identifying_centered_hexamers.tsv: Data file generated manually by editing T-number_capsids_squences.tsv to highlight the 3-fold hexamer-centered capsids screened with T_H.py.
• generate_shells.cxc: ChimeraX command script to generate 3D capsid models and snapshots centered on the 3-fold axis. Each capsid that one wants to render must be specified individually. The script was tested using ChimeraX version 1.2.
• ChimeraX_rendering_instructions_EMDB_capsid.md: Markdown file containing the instructions on how to generate the rendering of the SIO-2 procapsid, which was used as an empirical example of 3-fold hexamer centered capsid. Other EM maps can be rendered analogously.