After creating or finding variants using Protein Design, a common situation is the desire to visualize the environment around the variant. You may want to know how the new sidechain fits in its environment, and whether or not it changes the rotamer of any other residues.

Protean 3D allows you to easily locate neighboring residues using the “select neighbors” function. This function changes an existing selection to one consisting of those residues adjacent to the original selection.

Note that the command can be used with any selection, so it is not necessary to create variants before using this functionality.

To locate “neighbors” of a current selection, do any of the following:

  • Choose the Structure > Select Neighbors command
  • Use the Select Neighbors tool ().

When a single residue is selected, neighbors include all adjacent residues. When multiple residues, a ligand or molecule are selected, neighbors might encompass interfacing groups of residues on an adjacent chain.

Once neighbors are selected, you may wish to change their display color for ease of recognition.

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