Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: only the free plugin: https://www.schrodinger.com/SchrodingerKNIMEFreeNodes. No Schrodinger installation]
This is a companion discussion topic for the original entry at https://kni.me/w/X7q9hMb8wAqDlFxa