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Type Python Script
Author(s) Gianluca Tomasello
License CC BY-NC-SA


This script detects waters molecules within a specified distance from the ligand.
Detected water molecules are shown as spheres.
Distances between water molecules and O or N atoms of ligand (potential H-bonds) are shown by dotted lines.
An output file containing a list of distance between waters and ligand atoms and the number of interactions is written in the main PyMol folder.


waters [ligand name, distance]

Required Arguments

  • ligand name = the ligand residue name
  • distance = max distance in Angstroms


example #1 on PDB structure (1C0L)

PyMOL>waters FAD, 2.8

Output in GUI of PyMol:

Total number of water molecules at 2.8 A from ligand FAD: 3 Number of water molecules that interact with ligand: 3 Number of interactions ..→

A Random PyMOL-generated Cover. See Covers.