Introduction
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.
Usage
waters [ligand name, distance]
Required Arguments
- ligand name = the ligand residue name
- distance = max distance in Angstroms
Examples
example #1 on PDB structure (1C0L)
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 ..→
