PyMOL Wiki - User contributions [en]

ShowLigandWaters

2013-09-02T09:54:34Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== 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)'''
<source lang="python">
PyMOL>waters FAD, 2.8
</source>
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

[[File:Example 1 FAD 1C0L.png|450px|example #1]]

== The Code ==

Copy the following text and save it as waters.py

<source lang="python">
# -*- 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.

Author: Gianluca Tomasello, Gianluca Molla
University of Insubria, Varese, Italy
09/02/2013
gianluca.molla@uninsubria.it

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)

</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T09:52:04Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== 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)'''
<source lang="python">
PyMOL>waters FAD, 2.8
</source>
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

[[File:Example 1 FAD 1C0L.png|450px|example #1]]

== The Code ==

Copy the following text and save it as waters.py

<source lang="python">
# -*- 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)

</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T09:49:35Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== Introduction ==
This script detects waters molecules within a specified distance from the ligand. 
Detected water molecules are shown as spheres. 
Distances between water<\b> molecules and O or N atoms of ligand (potential H-bonds) are shown by dotted lines 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)'''
<source lang="python">
PyMOL>waters FAD, 2.8
</source>
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

[[File:Example 1 FAD 1C0L.png|450px|example #1]]

== The Code ==

Copy the following text and save it as waters.py

<source lang="python">
# -*- 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)

</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T09:42:21Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== 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 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)'''
<source lang="python">
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

</source>

output file: waters.txt

<source lang="python">
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
</source>

[[File:Example 1 FAD 1C0L.png|450px|example #1]]

== The Code ==

Copy the following text and save it as waters.py

<source lang="python">
# -*- 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)

</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T09:28:23Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== 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)'''
<source lang="python">
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

</source>

output file: waters.txt

<source lang="python">
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
</source>

[[File:Example 1 FAD 1C0L.png|450px|example #1]]

== The Code ==

Copy the following text and save it as waters.py

<source lang="python">
# -*- 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)

</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T09:17:23Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== 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)'''
<source lang="python">
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

</source>

output file: waters.txt

<source lang="python">
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
</source>

[[File:Example 1 FAD 1C0L.png|450px|example #1]]

== The Code ==

Copy the following text and save it as waters.py

<source lang="python">
# -*- 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 share 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)

</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T09:16:58Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== 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)'''
<source lang="python">
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

</source>

output file: waters.py

<source lang="python">
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
</source>

[[File:Example 1 FAD 1C0L.png|450px|example #1]]

== The Code ==

Copy the following text and save it as waters.py

<source lang="python">
# -*- 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 share 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)

</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T09:14:39Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== 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)'''
<source lang="python">
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

</source>

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

[[File:Example 1 FAD 1C0L.png|450px|example #1]]

== The Code ==

Copy the following text and save it as pairwisedistances.py

<source lang="python">
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)
</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

File:Example 1 FAD 1C0L.png

2013-09-02T09:12:10Z

GianlucaTomasello:

ShowLigandWaters

2013-09-02T09:07:04Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

== 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'''
<source lang="python">
PyMOL>pairwise_dist 1efa and chain D, 1efa and chain B, 3, output=S, show=Y

1efa/D/DC/13/OP1 to 1efa/B/TYR/47/OH: 2.765
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/N: 2.983
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/CB: 2.928
1efa/D/DT/14/O4' to 1efa/B/ALA/57/CB: 2.827
1efa/D/DT/14/OP1 to 1efa/B/ASN/25/OD1: 2.858
1efa/D/DT/14/OP1 to 1efa/B/GLN/54/NE2: 2.996
1efa/D/DT/14/OP2 to 1efa/B/SER/21/OG: 2.517
1efa/D/DC/15/N4 to 1efa/B/GLN/18/NE2: 2.723
1efa/D/DA/16/N6 to 1efa/B/GLN/18/NE2: 2.931

Number of distances calculated: 9
</source>

[[File:pairwise1.png|450px|example #1]]

== The Code ==

Copy the following text and save it as pairwisedistances.py

<source lang="python">
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)
</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T08:56:21Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

This is a test page########

== 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'''
<source lang="python">
PyMOL>pairwise_dist 1efa and chain D, 1efa and chain B, 3, output=S, show=Y

1efa/D/DC/13/OP1 to 1efa/B/TYR/47/OH: 2.765
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/N: 2.983
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/CB: 2.928
1efa/D/DT/14/O4' to 1efa/B/ALA/57/CB: 2.827
1efa/D/DT/14/OP1 to 1efa/B/ASN/25/OD1: 2.858
1efa/D/DT/14/OP1 to 1efa/B/GLN/54/NE2: 2.996
1efa/D/DT/14/OP2 to 1efa/B/SER/21/OG: 2.517
1efa/D/DC/15/N4 to 1efa/B/GLN/18/NE2: 2.723
1efa/D/DA/16/N6 to 1efa/B/GLN/18/NE2: 2.931

Number of distances calculated: 9
</source>

[[File:pairwise1.png|450px|example #1]]

== The Code ==

Copy the following text and save it as pairwisedistances.py

<source lang="python">
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)
</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T08:52:21Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:GianlucaTomasello|Gianluca Tomasello]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]#############
}}

This is a test page########

== 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'''
<source lang="python">
PyMOL>pairwise_dist 1efa and chain D, 1efa and chain B, 3, output=S, show=Y

1efa/D/DC/13/OP1 to 1efa/B/TYR/47/OH: 2.765
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/N: 2.983
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/CB: 2.928
1efa/D/DT/14/O4' to 1efa/B/ALA/57/CB: 2.827
1efa/D/DT/14/OP1 to 1efa/B/ASN/25/OD1: 2.858
1efa/D/DT/14/OP1 to 1efa/B/GLN/54/NE2: 2.996
1efa/D/DT/14/OP2 to 1efa/B/SER/21/OG: 2.517
1efa/D/DC/15/N4 to 1efa/B/GLN/18/NE2: 2.723
1efa/D/DA/16/N6 to 1efa/B/GLN/18/NE2: 2.931

Number of distances calculated: 9
</source>

[[File:pairwise1.png|450px|example #1]]

== The Code ==

Copy the following text and save it as pairwisedistances.py

<source lang="python">
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)
</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T08:51:03Z

GianlucaTomasello:

{{Infobox script-repo
|type = script
|download =
|author = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

This is a test page##

== Introduction ==
Given any two selections, this script calculates and returns the pairwise distances between all atoms that fall within a defined distance.

Can be used to measure distances within the same chain, between different chains or different objects.

Distances can be restricted to sidechain atoms only and the outputs either displayed on screen or printed on file.

== Usage ==
pairwise_dist sel1, sel2, max_dist, [output=S/P/N, [sidechain=N/Y, [show=Y/N]]]

== Required Arguments ==
* '''sel1''' = first selection
* '''sel2''' = second selection
* '''max_dist''' = max distance in Angstroms

== Optional Arguments ==
* '''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)

== Examples ==
'''example #1'''
<source lang="python">
PyMOL>pairwise_dist 1efa and chain D, 1efa and chain B, 3, output=S, show=Y

1efa/D/DC/13/OP1 to 1efa/B/TYR/47/OH: 2.765
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/N: 2.983
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/CB: 2.928
1efa/D/DT/14/O4' to 1efa/B/ALA/57/CB: 2.827
1efa/D/DT/14/OP1 to 1efa/B/ASN/25/OD1: 2.858
1efa/D/DT/14/OP1 to 1efa/B/GLN/54/NE2: 2.996
1efa/D/DT/14/OP2 to 1efa/B/SER/21/OG: 2.517
1efa/D/DC/15/N4 to 1efa/B/GLN/18/NE2: 2.723
1efa/D/DA/16/N6 to 1efa/B/GLN/18/NE2: 2.931

Number of distances calculated: 9
</source>

[[File:pairwise1.png|450px|example #1]]

'''example #2'''
<source lang="python">
PyMOL>pairwise_dist 2w8s and chain a, 2W8s and chain b, 3, sidechain=Y, output=S, show=Y

2W8S/A/GLN/432/OE1 to 2W8S/B/ARG/503/NH2: 2.758
2W8S/A/ASP/434/OD1 to 2W8S/B/SER/493/OG: 2.444
2W8S/A/TYR/447/OH to 2W8S/B/GLN/485/NE2: 2.878
2W8S/A/HIS/449/NE2 to 2W8S/B/SER/489/OG: 2.686
2W8S/A/GLN/485/OE1 to 2W8S/B/TYR/447/OH: 2.971
2W8S/A/SER/489/OG to 2W8S/B/HIS/449/NE2: 2.913
2W8S/A/SER/493/OG to 2W8S/B/ASP/434/OD1: 2.491
2W8S/A/ARG/503/NH2 to 2W8S/B/GLN/432/OE1: 2.653

Number of distances calculated: 8
</source>

[[File:pairwise2.png|450px|example #2]]

'''example #3'''
<source lang="python">
PyMOL>pairwise_dist 1FOS and chain H and resi 290:300, 1FOS and chain G, 4, sidechain=Y, show=Y, output=P

Results saved in IntAtoms_4.txt
Number of distances calculated: 24
</source>

[[File:pairwise3.png|450px|example #3]]

== The Code ==

Copy the following text and save it as pairwisedistances.py

<source lang="python">
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)
</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

ShowLigandWaters

2013-09-02T08:02:05Z

GianlucaTomasello: Created page with "{{Infobox script-repo |type = script |download = |author = Pietro Gatti-Lafranconi |license = [http://creativecommons.org/licenses/by-n..."

{{Infobox script-repo
|type = script
|download =
|author = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
}}

This is a test page

== Introduction ==
Given any two selections, this script calculates and returns the pairwise distances between all atoms that fall within a defined distance.

Can be used to measure distances within the same chain, between different chains or different objects.

Distances can be restricted to sidechain atoms only and the outputs either displayed on screen or printed on file.

== Usage ==
pairwise_dist sel1, sel2, max_dist, [output=S/P/N, [sidechain=N/Y, [show=Y/N]]]

== Required Arguments ==
* '''sel1''' = first selection
* '''sel2''' = second selection
* '''max_dist''' = max distance in Angstroms

== Optional Arguments ==
* '''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)

== Examples ==
'''example #1'''
<source lang="python">
PyMOL>pairwise_dist 1efa and chain D, 1efa and chain B, 3, output=S, show=Y

1efa/D/DC/13/OP1 to 1efa/B/TYR/47/OH: 2.765
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/N: 2.983
1efa/D/DC/13/OP2 to 1efa/B/LEU/6/CB: 2.928
1efa/D/DT/14/O4' to 1efa/B/ALA/57/CB: 2.827
1efa/D/DT/14/OP1 to 1efa/B/ASN/25/OD1: 2.858
1efa/D/DT/14/OP1 to 1efa/B/GLN/54/NE2: 2.996
1efa/D/DT/14/OP2 to 1efa/B/SER/21/OG: 2.517
1efa/D/DC/15/N4 to 1efa/B/GLN/18/NE2: 2.723
1efa/D/DA/16/N6 to 1efa/B/GLN/18/NE2: 2.931

Number of distances calculated: 9
</source>

[[File:pairwise1.png|450px|example #1]]

'''example #2'''
<source lang="python">
PyMOL>pairwise_dist 2w8s and chain a, 2W8s and chain b, 3, sidechain=Y, output=S, show=Y

2W8S/A/GLN/432/OE1 to 2W8S/B/ARG/503/NH2: 2.758
2W8S/A/ASP/434/OD1 to 2W8S/B/SER/493/OG: 2.444
2W8S/A/TYR/447/OH to 2W8S/B/GLN/485/NE2: 2.878
2W8S/A/HIS/449/NE2 to 2W8S/B/SER/489/OG: 2.686
2W8S/A/GLN/485/OE1 to 2W8S/B/TYR/447/OH: 2.971
2W8S/A/SER/489/OG to 2W8S/B/HIS/449/NE2: 2.913
2W8S/A/SER/493/OG to 2W8S/B/ASP/434/OD1: 2.491
2W8S/A/ARG/503/NH2 to 2W8S/B/GLN/432/OE1: 2.653

Number of distances calculated: 8
</source>

[[File:pairwise2.png|450px|example #2]]

'''example #3'''
<source lang="python">
PyMOL>pairwise_dist 1FOS and chain H and resi 290:300, 1FOS and chain G, 4, sidechain=Y, show=Y, output=P

Results saved in IntAtoms_4.txt
Number of distances calculated: 24
</source>

[[File:pairwise3.png|450px|example #3]]

== The Code ==

Copy the following text and save it as pairwisedistances.py

<source lang="python">
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)
</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]