Development of a New Program, CAPAXIS, for Analysis on Structures of Icosahedrally Symmetric Virus Capsids

Abstract

An icosahedrally symmetric virus capsid is a molecular assembly of 60 identical protomers. Therefore, geometrical analysis on rotation axes, protomer position, etc., in icosahedral symmetry is always needed for preparation and analysis of simulation of icosahedrally symmetric capsids. This analysis is simple, but is not possible without detailed knowledge of geometrical properties of icosahedral symmetry. The author developed a new program, CAPAXIS, for the purpose to analyze geometrical properties, using the standard rotation matrices and rotation axes, the partition planes, the partition tables, the cell number function, etc., which have been clarified through the authors' development of rotational symmetry boundary condition. CAPAXIS has an UNIX-like command interface and can perform various calculations following the command line parameters. CAPAXIS is developed as free software following the GNU license. Classifications of the coordinate systems adopted for all the 85 files of icosahedrally symmetric capsid structure deposited to the Protein Databank are analyzed by CAPAXIS and the coordinate systems were classified into 3 groups.