Show contacts

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Type PyMOL Plugin
Download plugins/
Author(s) David Ryan Koes
License CC BY 4.0
This code has been put under version control in the project Pymol-script-repo


PyMOL Plugin for displaying polar contacts. Good hydrogen bonds (as determined by PyMOL) are shown in yellow. Electrostatic clashes (donor-donor or acceptor-acceptor) are shown in red. Close (<4.0 A) but not ideal contacts are shown in purple. Cutoffs are configurable. Exports the command `contacts` which takes two selections and an optional name for the generated contacts group. Alternatively, the selections can be chosen using a dialog box accessible from the Plugins menu.


show_contacts sel1, sel2, result="contacts", cutoff=3.6, bigcutoff=4.0

Required Arguments

  • sel1 = first selection
  • sel2 = second selection

Optional Arguments

  • result = name of created group containing contacts
  • cutoff = cutoff for good contacts (yellow dashes)
  • bigcutoff = cutoff for suboptimal contacts (purple dashes)