I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
I recommend using software called ChemCraft. The software isn't free; however, they offer a 150 day trial period. I typically use this program to open formatted checkpoint files from Gaussian calculations to view orbitals. It has plenty of other functions, including the ability to open multiple .xyz files and save multiple images.
The default colors are a bit yucky, but I recommend using one of the following from the Display menu: CPK, GaussView, or Spartan. Those will color atoms with the typical scheme: Nitrogen (blue), Oxygen (red), etc.
I hope this helps!