Virus particle sizes
======================

Virus particles (capsids) are made up of many identical protein units
and are often extremely symmetrical. For this reason, both when
determining virus structures and when representing them in the PDB
archive, not all coordinates of the atoms are reported, and not even
all coordinates of the independent crystal atoms (the asymmetric unit),
but only those coordinates the atoms from which all remaining atoms
can be restored with the help of the symmetry operators. The symmetry
operators themselves are also specified in special entries in PDB
files [1].

To find out any structural features of virus particles
characteristics, in particular those not specified in the PDB file,
coordinates of all atoms should be reconstructed and analysed. This
can be done by applying symmetry operators specified in the PDB file.

Questions:

- how many virus particle structures are there in the PDB archive? How
  many of them are icosahedral? Describe and discuss search methods
  that are possible.

- What are the particle sizes of the viruses described in the PDB
  archive? What are the sizes of the icosahedral virus particles
  (their diameters)? What are the distributions of these parameters?
  How it depends on the viral nucleic acid (n.r.) length/mass? What is
  the density of the n.a. packed in the virus capsid? Is it same for
  all viruses, do you notice any trends?

- Is the density of the internal nucleic acid of the viral capsid
  similar to that of the protein globule density (find the value of
  this density in the literature)? Is he depends on whether the virus
  uses DNA or RNA; or nucleic acid single strand or double strand?

Program:

This study requires a program that reads PDB archive files, finds in
them the matrices for the restoration of the biological particle,
applies them atoms and determines the size of the particle. What
matrices will you apply? What kind parameter or parameters you will
use as the capsid size (parameters have be informative, on the one
hand, but also easy to calculate, on the other hand)? For debugging
and program verification purposes, you should provide an option to
output all generated atoms in an appropriate format.

Links:

1. Protein Data Bank. Introduction to Biological Assemblies and the
   PDB Archives. [viewed 02/25/2020] URL:
   https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies