ShowLigandWaters

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)

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 between water molecules and ligand: 4

output file: waters.txt

HOH residue 2002 -- and -- ['FAD', '1363', 'O1P'] ---> 2.611289 A HOH residue 2002 -- and -- ['FAD', '1363', 'O5B'] ---> 3.592691 A HOH residue 2008 -- and -- ['FAD', '1363', 'O1A'] ---> 2.678604 A HOH residue 2009 -- and -- ['FAD', '1363', 'O2P'] ---> 2.643039 A

---

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 between water molecules and ligand: 4

The Code

Copy the following text and save it as waters.py

# -*- coding: cp1252 -*-
"""
This script detects waters molecules within a specified distance from the ligand.
Water molecules are shown.
Distance between water molecules and O or N atoms of ligand are shown.

Usage
waters, [ligand name, distance]

Parameters

ligand : the ligand residue name 

distance : a float number that specify the maximum distance from the ligand to consider the water molecule
           
Output
-A file is produced containing a list of distance between waters and ligand atoms and the number of interactions
-A graphic output show the water molecules interacting whith the ligand atoms by showing the distances between them
"""

from pymol import cmd,stored
#define function: waters
def waters(ligand, distance):
    stored.HOH = [] 
    cmd.set('label_color','white') 
    cmd.delete ("sele")
    cmd.hide ("everything")
    cmd.show_as ("sticks", "resn %s" % ligand)
    #iterate all water molecules nearby the ligand
    cmd.iterate('resn %s around %s and resn HOH' % (ligand,distance),'stored.HOH.append(resi)') 
    f = open("waters.txt","a")
    count=0
    count_int=0
    
    for i in range(0,len(stored.HOH)):        
        cmd.distance('dist_HOH_FAD', 'resi ' + stored.HOH[i], '(resn %s and n. O*+N*) w. 3.6 of resi %s'% (ligand, stored.HOH[i]))
        stored.name = []
        #iterate all ligand atoms within a predetermined distance from the water molecule
        cmd.iterate('(resn %s and n. O*+N*) w. 3.6 of resi %s'% (ligand, stored.HOH[i]),'stored.name.append([resn,resi,name])') 

        if stored.name:           
            count = count+1
            count_int = count_int+len(stored.name)

        for j in range(0,len(stored.name)):            
            cmd.select('base', 'resi ' + stored.HOH[i])
            cmd.select('var','resn '+ligand+ ' and n. ' + stored.name[j][2]) 
            #calculate the distance between a specific atom and the water molecule
            dist = cmd.get_distance('base','var')            
            f.write('HOH residue %s -- and -- %s  --->  %f A\n'%(stored.HOH[i],stored.name[j], dist))  

    cmd.select ("waters","resn %s around %s and resn HOH" % (ligand,distance))
    cmd.show_as ("spheres", "waters")
    cmd.zoom ("visible")
    num_atm = cmd.count_atoms ("waters")
    print ("Total number of water molecules at %s A from ligand %s: %s \n" % (distance,ligand,num_atm))
    print ("Number of water molecules that interact with ligand: %d\n" % (count))
    print ("Number of interactions between water molecules and ligand: %d\n" % count_int)
    f.write('-------------------------------------------------------------\n')
    f.write("Total number of water molecules at %s A from ligand %s: %s \n" % (distance,ligand,num_atm))
    f.write("Number of water molecules that interact with ligand: %d\n" % count)
    f.write("Number of interactions between water molecules and ligand: %d\n\n\n\n" % count_int)
    f.close()
    cmd.delete ("waters")
    
cmd.extend("waters",waters)