Define interaction Atom Sets Dialog Box

noncovalent bonds, contacts, pi interactions, hydrogen bonds, halogen bonds, pi-pi stacking, pi-cation, salt bridges H-bonds

Define sets of atoms for which interactions are displayed in the Workspace. You can define a single set of atoms for display of interactions within the set, or one or more pairs of atom sets for display of interactions between the atom sets in the pair.

To open this dialog box, choose Other from the interacting atom set option menu in the Interactions Toolbox.

  • Features
  • Additional Resources

Define interaction Atom Sets Dialog Box Features

Use multiple pairings option

Select this option if you want to define multiple pairs of atom sets ("pairings"), to display interactions between the atom sets in each pair. For example, if you have multiple aligned complexes in the Workspace and want to see only the interactions between each receptor and its ligand, the receptor and the ligand would be defined as a pair of atom sets for each complex.

Add button

Add another pairing to the list of pairings. A new label is added in the pairings list, and the Atom set N picking tools are cleared ready for definition of new sets.

Pairings list and Delete button

Lists the defined pairings of atom sets that form a group whose interactions are displayed. Each is labeled Pair X, where X is a letter starting from A. You can select a single pairing in the list and edit it or delete it with the Delete button.

Atom set N picking tools

Specify the atoms that are in each set, using the standard picking tools. If you are not using multiple pairings, you can specify just atom set 1 to display intra-set interactions; otherwise specify the atoms in each set to display interactions between the atoms in set 1 and the atoms in set 2.

Same for all interactions option

Apply the atom sets defined for the target interaction type to interactions of all types.

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