Since I had many AViz files to process, I developed a few python scripts to process them automatically:

  1. A script to translate all atoms in a file around a new center.
  2. A script to remove any atoms outside of a box around (0, 0, 0).
  3. A script that combines `` and ``, with an additional option to return the file to its original coordinates after the filtering.
  4. A script to keep only atoms of certain type(s).
  5. A script that returns some statistics about the AViz file (list of different atoms, range of coordinates).
  6. Full Example: Walk-through example of how to use the python scripts

I also developed a small framework to help write these scripts in a more streamlined fashion. The scripts are available to download at this link.