The basic idea of block_atom is to get an ALCHEMY data file which combines both atomic and block representations of nucleic-acid-containing structure in PDB format. The ALCHEMY file can then be displayed interactively using RasMol (v2.6.4, by its original author) (or Jmol).
Again, the point is best illustrated with an example. Here I am using 355d, the famous Drew-Dickerson B-DNA dodecamer solved at a high resolution by Williams and colleagues. Let the input PDB file be 355d.pdb, then the output file is automatically named 355d.alc, which can be displayed using RasMol with the options '-alchemy -noconnect'.
block_atom 355d.pdbOne view of RasMol rendered image is as below, which shows more clearly the minor-groove (colored blue) of the DNA duplex and the various intra-base-pair deformations (e.g., propeller and buckle):
rasmol -alchemy -noconnect 355d.alc
I initially wrote this utility script mostly for verification purpose, i.e., to make sure that the base reference frames are defined properly. For those who want to know more about 3DNA, having a look of the script (which is tiny) and understanding how it works could be a good exercise.