Some functionality in Discovery Studio that is often overlooked are the scripts available under the Scripts menu. These provided scripts are divided into different categories - Visualization, Selection, Structure Editing, Ligand Interactions and Sequences. The Visualization section includes scripts for hiding and showing different types of molecule and also for setting the display. A particularly useful script is ‘Publication Quality’, which sets the graphics for quickly preparing the system for publication quality images with modified material and projection settings and a white background.

Under Structure Editing, other highlights include ‘Molecules to Conformations’ (to produce a set of conformations to process with trajectory based tools) and ‘Conformations to Molecules’ to split conformations into separate molecules. The PDB Ligand Bond Orders script is also helpful for setting the bond orders of small molecules to match the PDB ligand definitions, saving time from checking and making changes manually.