Settings

In the Settings button of the main menu, the “Binding Site Settings” section includes a checkbox labeled “Show all objects in binding sites”. When this option is checked, it allows all objects loaded in PyMOL to be displayed in the binding site selection lists for NRGRank, IsoMIF, and FlexAID. This functionality is necessary when working with pre-calculated binding sites from previous projects.

In the “Multi-state Object Manager”, the user can combine and split multi-state objects. Press “Refresh” to list all objects loaded in PyMOL. To combine objects into a single multi-state object, select all objects to be combined in the list, write the name of the combined object, and press “Combine Objects”.

To split states of a multi-state object, select it in the list and press “Split States”. For mutants generated using the “Single Mutations” functionality, the user can choose the wild type and all objects generated will be renamed according to their differences from the wild type reference.