ShowLigandWaters

Introduction

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 and is maked an output file containing a list of distance between waters and ligand atoms and the number of interactions

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

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.py

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 pairwisedistances.py

from pymol import cmd, stored, math

def pairwise_dist(sel1, sel2, max_dist, output="N", sidechain="N", show="N"):
	"""
	usage: pairwise_dist sel1, sel2, max_dist, [output=S/P/N, [sidechain=N/Y, [show=Y/N]]]
	sel1 and sel2 can be any to pre-existing or newly defined selections
	max_dist: maximum distance in Angstrom between atoms in the two selections
	--optional settings:
	output: accepts Screen/Print/None (default N)
	sidechain: limits (Y) results to sidechain atoms (default N)
	show: shows (Y) individual distances in pymol menu (default=N)
	"""
	print ""
	cmd.delete ("dist*")
	extra=""
	if sidechain=="Y": extra=" and not name c+o+n"
	
	#builds models
	m1=cmd.get_model(sel2+" around "+str(max_dist)+" and "+sel1+extra)
	m1o=cmd.get_object_list(sel1)
	m2=cmd.get_model(sel1+" around "+str(max_dist)+" and "+sel2+extra)
	m2o=cmd.get_object_list(sel2)

	#defines selections
	cmd.select("__tsel1a", sel1+" around "+str(max_dist)+" and "+sel2+extra)
	cmd.select("__tsel1", "__tsel1a and "+sel2+extra)
	cmd.select("__tsel2a", sel2+" around "+str(max_dist)+" and "+sel1+extra)
	cmd.select("__tsel2", "__tsel2a and "+sel1+extra)
	cmd.select("IntAtoms_"+max_dist, "__tsel1 or __tsel2")
	cmd.select("IntRes_"+max_dist, "byres IntAtoms_"+max_dist)
 
	#controlers-1
	if len(m1o)==0: 
		print "warning, '"+sel1+extra+"' does not contain any atoms."
		return
	if len(m2o)==0: 
		print "warning, '"+sel2+extra+"' does not contain any atoms."
		return
	
	#measures distances
	s=""
	counter=0
	for c1 in range(len(m1.atom)):
		for c2 in range(len(m2.atom)):
			distance=math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))
			if distance<float(max_dist):
				s+="%s/%s/%s/%s/%s to %s/%s/%s/%s/%s: %.3f\n" % (m1o[0],m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2o[0],m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
				counter+=1
				if show=="Y": cmd.distance (m1o[0]+" and "+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, m2o[0]+" and "+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)

	#controler-2
	if counter==0: 
		print "warning, no distances were measured! Check your selections/max_dist value"
		return
	
	#outputs
	if output=="S": print s
	if output=="P":
		f=open('IntAtoms_'+max_dist+'.txt','w')
		f.write("Number of distances calculated: %s\n" % (counter))
		f.write(s)
		f.close()
		print "Results saved in IntAtoms_%s.txt" % max_dist
	print "Number of distances calculated: %s" % (counter)
	cmd.hide("lines", "IntRes_*")
	if show=="Y": cmd.show("lines","IntRes_"+max_dist)
	cmd.deselect()
  
cmd.extend("pairwise_dist", pairwise_dist)