PyMOL Wiki - User contributions [en]

Load new B-factors

2014-09-22T15:43:54Z

PietroGattiLafranconi: download link added

{{Infobox script-repo
|type = script
|download = [http://dx.doi.org/10.6084/m9.figshare.1176991 figshare]
|author = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
|license = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
}}

== Introduction ==
Quick and simple script to replace B-factor values in a PDB structure.

New B-factors are provided in an external .txt file, one per line.

By default, the script will also redraw the selected molecule as cartoon putty and colour by B-factor

== Usage ==
loadBfacts mol, [startaa, [source, [visual Y/N]]]

== Required Arguments ==
* '''mol ''' = any object selection (within one single object though)

== Optional Arguments ==
* '''startaa''' = number of amino acid the first value in 'source' refers to (default=1)
* '''source''' = name of the file containing new B-factor values (default=newBfactors.txt)
* '''visual''' = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)

== Limitations ==
For its very nature, this script is not suitable for complex cases in which only some B-factors are to be replaced, or on complex selections. In such cases, [http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ data2bfactor.py] is a better choice.

B-factors have to be entered one per line, with no labels or amino acid ID. They will replace values of a continuous stretch of amino acids of equal length (or shorter) starting from the position provided with 'startaa'.

'newBfactors.txt' looks like
2
0
0
3
7
...

== Examples ==
<source lang="python">
PyMOL>loadbfacts 1LVM
</source>
[[File:LoadBfacts1.png|450px|example #1]]

<source lang="python">
PyMOL>loadbfacts 1LVM and chain a, startaa=135
</source>
[[File:LoadBfacts02.png|450px|example #2]]

== The Code ==
<source lang="python">
from pymol import cmd, stored, math

def loadBfacts (mol,startaa=1,source="newBfactors.txt", visual="Y"):
"""
Replaces B-factors with a list of values contained in a plain txt file

usage: loadBfacts mol, [startaa, [source, [visual]]]

mol = any object selection (within one single object though)
startaa = number of first amino acid in 'new B-factors' file (default=1)
source = name of the file containing new B-factor values (default=newBfactors.txt)
visual = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)

example: loadBfacts 1LVM and chain A
"""
obj=cmd.get_object_list(mol)[0]
cmd.alter(mol,"b=-1.0")
inFile = open(source, 'r')
counter=int(startaa)
bfacts=[]
for line in inFile.readlines():
bfact=float(line)
bfacts.append(bfact)
cmd.alter("%s and resi %s and n. CA"%(mol,counter), "b=%s"%bfact)
counter=counter+1
if visual=="Y":
cmd.show_as("cartoon",mol)
cmd.cartoon("putty", mol)
cmd.set("cartoon_putty_scale_min", min(bfacts),obj)
cmd.set("cartoon_putty_scale_max", max(bfacts),obj)
cmd.set("cartoon_putty_transform", 0,obj)
cmd.set("cartoon_putty_radius", 0.2,obj)
cmd.spectrum("b","rainbow", "%s and n. CA " %mol)
cmd.ramp_new("count", obj, [min(bfacts), max(bfacts)], "rainbow")
cmd.recolor()

cmd.extend("loadBfacts", loadBfacts);
</source>

[[Category:Script_Library]]
[[Category:Biochemical_Scripts]]
[[Category:Coloring]]
[[Category:Structural_Biology_Scripts]]

Load new B-factors

2014-09-22T15:38:19Z

PietroGattiLafranconi: Page created

{{Infobox script-repo
|type = script
|download = TBC
|author = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
|license = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
}}

== Introduction ==
Quick and simple script to replace B-factor values in a PDB structure.

New B-factors are provided in an external .txt file, one per line.

By default, the script will also redraw the selected molecule as cartoon putty and colour by B-factor

== Usage ==
loadBfacts mol, [startaa, [source, [visual Y/N]]]

== Required Arguments ==
* '''mol ''' = any object selection (within one single object though)

== Optional Arguments ==
* '''startaa''' = number of amino acid the first value in 'source' refers to (default=1)
* '''source''' = name of the file containing new B-factor values (default=newBfactors.txt)
* '''visual''' = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)

== Limitations ==
For its very nature, this script is not suitable for complex cases in which only some B-factors are to be replaced, or on complex selections. In such cases, [http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ data2bfactor.py] is a better choice.

B-factors have to be entered one per line, with no labels or amino acid ID. They will replace values of a continuous stretch of amino acids of equal length (or shorter) starting from the position provided with 'startaa'.

'newBfactors.txt' looks like
2
0
0
3
7
...

== Examples ==
<source lang="python">
PyMOL>loadbfacts 1LVM
</source>
[[File:LoadBfacts1.png|450px|example #1]]

<source lang="python">
PyMOL>loadbfacts 1LVM and chain a, startaa=135
</source>
[[File:LoadBfacts02.png|450px|example #2]]

== The Code ==
<source lang="python">
from pymol import cmd, stored, math

def loadBfacts (mol,startaa=1,source="newBfactors.txt", visual="Y"):
"""
Replaces B-factors with a list of values contained in a plain txt file

usage: loadBfacts mol, [startaa, [source, [visual]]]

mol = any object selection (within one single object though)
startaa = number of first amino acid in 'new B-factors' file (default=1)
source = name of the file containing new B-factor values (default=newBfactors.txt)
visual = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)

example: loadBfacts 1LVM and chain A
"""
obj=cmd.get_object_list(mol)[0]
cmd.alter(mol,"b=-1.0")
inFile = open(source, 'r')
counter=int(startaa)
bfacts=[]
for line in inFile.readlines():
bfact=float(line)
bfacts.append(bfact)
cmd.alter("%s and resi %s and n. CA"%(mol,counter), "b=%s"%bfact)
counter=counter+1
if visual=="Y":
cmd.show_as("cartoon",mol)
cmd.cartoon("putty", mol)
cmd.set("cartoon_putty_scale_min", min(bfacts),obj)
cmd.set("cartoon_putty_scale_max", max(bfacts),obj)
cmd.set("cartoon_putty_transform", 0,obj)
cmd.set("cartoon_putty_radius", 0.2,obj)
cmd.spectrum("b","rainbow", "%s and n. CA " %mol)
cmd.ramp_new("count", obj, [min(bfacts), max(bfacts)], "rainbow")
cmd.recolor()

cmd.extend("loadBfacts", loadBfacts);
</source>

[[Category:Script_Library]]
[[Category:Biochemical_Scripts]]
[[Category:Coloring]]
[[Category:Structural_Biology_Scripts]]

ListSelection2

2014-05-22T16:59:19Z

PietroGattiLafranconi: download link and license update

{{Infobox script-repo
|type = script
|download = [http://dx.doi.org/10.6084/m9.figshare.1031599 figshare]
|author = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
|license = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
}}

= Overview =
Alternative script to [[List_Selection]] that will:
* list multiple residues once
* include water and hetatoms
* account for different chains/objects
* produce a screen/printed output

= Usage =
<source lang="python">
listselection selection, [output=N/S/P, [HOH=Y/N ]]
</source>
where:
* '''selection''' can be any existing or newly-defined selection
* '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
* '''HOH''' (default Y) allows to exclude (N) water residues from the list

= Examples =
<source lang="python">
PyMOL>listselection 1efa, output=P
Residues in '1efa': 1043
Results saved in listselection_1efa.txt
</source>

<source lang="python">
PyMOL>listselection sele, output=S, HOH=N
Residues in 'sele, without HOH': 7
1LBH/A/ARG/86
1LBH/A/ALA/87
1LBH/A/ASP/88
1LBH/A/GLN/89
1LBH/A/LEU/90
1LBH/A/GLY/91
1LBH/A/ALA/92
</source>

<source lang="python">
PyMOL>listselection 1efa and resn LEU, output=S
Residues in '1efa and resn LEU': 108
1efa/A/LEU/6
1efa/A/LEU/45
1efa/A/LEU/56
[...]
1efa/C/LEU/323
1efa/C/LEU/330
</source>

= Code =
Copy the following text and save it as listselection.py

<source lang="python">
from pymol import cmd, stored

def listselection (selection, output="N", HOH="Y"):
"""
usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]

More information at: PymolWiki: http://http://pymolwiki.org/index.php/ListSelection2
AUTHOR: Pietro Gatti-Lafranconi, 2013
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""
printedselection=""
extra=""
counter=0
sel=selection
objs=cmd.get_object_list(sel)

if HOH=="N":
sel=selection+" and not resn HOH"
extra=", without HOH"

for a in range(len(objs)):
m1=cmd.get_model(sel+" and "+objs[a])
for x in range(len(m1.atom)):
if m1.atom[x-1].resi!=m1.atom[x].resi:
printedselection+="%s/%s/%s/%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resn, m1.atom[x].resi)
counter+=1

print "Residues in '%s%s': %s" % (selection, extra, counter)
if output=="S": print printedselection
if output=="P":
f=open('listselection_'+selection+'.txt','w')
f.write("Residues in '%s%s': %s\n" % (selection, extra, counter))
f.write(printedselection)
f.close()
print "Results saved in listselection_%s.txt" % selection

cmd.extend('listselection',listselection)
</source>

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

Pairwise distances

2014-05-22T16:59:03Z

PietroGattiLafranconi: download link and license update

{{Infobox script-repo
|type = script
|download = [http://dx.doi.org/10.6084/m9.figshare.1031600 figshare]
|author = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
|license = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
}}

== 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]]

DistancesRH

2014-05-22T16:56:10Z

PietroGattiLafranconi: download link and license update

{{Infobox script-repo
|type = script
|download = [http://dx.doi.org/10.6084/m9.figshare.1031580 figshare]
|author = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
|license = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==
distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

== Required Arguments ==
* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
'''example #1'''
<source lang="python">
distancesRH 2WHH, 25, 3.2, show=Y
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen (figure 1, left).
<source lang="python">
distancesRH 2WHH, 25, 3.2, show=Y, aname=OD1, output=P
</source>
Same result as before, but only distances from atom OD1 are measured and shown. Results will be printed in 'distancesRH_25-OD1.txt' (figure 1, right).

[[File:distancesRH_ex1.png|450px|example #1]]

'''example #2'''
<source lang="python">
distancesRH 1EFA, 901, 3.5, show=Y
</source>
Will show distances between all atoms in resi 901 of 1EFA and all atoms within 3.5 Å (figure 2, left).
<source lang="python">
distancesRH 1EFA, 901, 3.5, show=Y, Hbonds=Y
</source>
Distances will now be calculated between atoms that can form H bonds only (figure 2, right).

[[File:distancesRH_ex2.png|450px|example #2]]

'''example #3'''
<source lang="python">
distancesRH 1EFA, 18, 4.7, chain=B, show=Y, aname=NE2
</source>
Distances between atom NE2 of residue 19 in chain B of 1EFA and all atoms within 4.7 Å (all of which are in the DNA fragment of chain D, figure 3).

[[File:distancesRH_ex3.png|300px|example #3]]

== Notes, Further Developments and Requests ==
* This script works with visible objects (handling of multiple states will hopefully be implemented soon)
* As it is intended to be user-friendly more than fast, this script is not suitable to calculate distances between large objects. Use [[Quick_dist]] instead.

== Updates ==
* '''11/01/2013''' - edit #1: ''distances measured between different chains''
* '''13/01/2013''' - edit #2: ''print output optimsed''

== The Code ==

Copy the following text and save it as distancesRH.py

<source lang="python">

"""
DESCRIPTION
Given an object, a reference amino acid and a radius, this scripts calculates pairwise
distances between all atoms in the reference and all atoms that fall within the given range.
Distances are either returned on screen (default) or printed on file.
Distances can be calculated from a single atom only.
Optionally, only atoms that can form H-bonds can be returned (but check distances!)

More information at: PymolWiki
http://pymolwiki.org/index.php/DistancesRH

AUTHOR
Pietro Gatti-Lafranconi, 2012
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+obj)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
if aname=="*": aname="ALL"
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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

User:PietroGattiLafranconi

2014-04-25T17:02:42Z

PietroGattiLafranconi:

* Contributed [[DistancesRH]], [[ListSelection2]] and [[Pairwise_distances]]
* Will be happy to receive feedbacks/suggestions
* can be found [http://www2.bio.cam.ac.uk/~fhlab/pg356.php here]

User:PietroGattiLafranconi

2014-01-08T17:59:56Z

PietroGattiLafranconi: link updated

* Is new to PyMOLWiki
* Submitted [[DistancesRH]], [[ListSelection2]] and [[Pairwise_distances]]
* Will be happy to receive feedbacks/suggestions
* can be found [www2.bio.cam.ac.uk/~fhlab/pg356.php here]

Pairwise distances

2013-07-24T17:56:54Z

PietroGattiLafranconi:

User:PietroGattiLafranconi

2013-07-24T17:53:59Z

PietroGattiLafranconi:

* Is new to PyMOLWiki
* Submitted [[DistancesRH]], [[ListSelection2]] and [[Pairwise_distances]]
* Will be happy to receive feedbacks/suggestions
* can be found [http://www.bio.cam.ac.uk/~fhlab/members/pg356.shtml here]

Pairwise distances

2013-07-24T17:52:23Z

PietroGattiLafranconi: page created

File:Pairwise3.png

2013-07-24T17:50:27Z

PietroGattiLafranconi:

File:Pairwise2.png

2013-07-24T17:50:17Z

PietroGattiLafranconi:

File:Pairwise1.png

2013-07-24T17:49:39Z

PietroGattiLafranconi:

ListSelection2

2013-03-14T15:45:56Z

PietroGattiLafranconi:

{{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]
}}

= Overview =
Alternative script to [[List_Selection]] that will:
* list multiple residues once
* include water and hetatoms
* account for different chains/objects
* produce a screen/printed output

= Usage =
<source lang="python">
listselection selection, [output=N/S/P, [HOH=Y/N ]]
</source>
where:
* '''selection''' can be any existing or newly-defined selection
* '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
* '''HOH''' (default Y) allows to exclude (N) water residues from the list

= Examples =
<source lang="python">
PyMOL>listselection 1efa, output=P
Residues in '1efa': 1043
Results saved in listselection_1efa.txt
</source>

<source lang="python">
PyMOL>listselection sele, output=S, HOH=N
Residues in 'sele, without HOH': 7
1LBH/A/ARG/86
1LBH/A/ALA/87
1LBH/A/ASP/88
1LBH/A/GLN/89
1LBH/A/LEU/90
1LBH/A/GLY/91
1LBH/A/ALA/92
</source>

<source lang="python">
PyMOL>listselection 1efa and resn LEU, output=S
Residues in '1efa and resn LEU': 108
1efa/A/LEU/6
1efa/A/LEU/45
1efa/A/LEU/56
[...]
1efa/C/LEU/323
1efa/C/LEU/330
</source>

= Code =
Copy the following text and save it as listselection.py

<source lang="python">
from pymol import cmd, stored

def listselection (selection, output="N", HOH="Y"):
"""
usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]

More information at: PymolWiki: http://http://pymolwiki.org/index.php/ListSelection2
AUTHOR: Pietro Gatti-Lafranconi, 2013
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""
printedselection=""
extra=""
counter=0
sel=selection
objs=cmd.get_object_list(sel)

if HOH=="N":
sel=selection+" and not resn HOH"
extra=", without HOH"

for a in range(len(objs)):
m1=cmd.get_model(sel+" and "+objs[a])
for x in range(len(m1.atom)):
if m1.atom[x-1].resi!=m1.atom[x].resi:
printedselection+="%s/%s/%s/%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resn, m1.atom[x].resi)
counter+=1

print "Residues in '%s%s': %s" % (selection, extra, counter)
if output=="S": print printedselection
if output=="P":
f=open('listselection_'+selection+'.txt','w')
f.write("Residues in '%s%s': %s\n" % (selection, extra, counter))
f.write(printedselection)
f.close()
print "Results saved in listselection_%s.txt" % selection

cmd.extend('listselection',listselection)
</source>

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

ListSelection2

2013-03-14T15:44:06Z

PietroGattiLafranconi:

= Overview =
Alternative script to [[List_Selection]] that will:
* list multiple residues once
* include water and hetatoms
* account for different chains/objects
* produce a screen/printed output

= Usage =
<source lang="python">
listselection selection, [output=N/S/P, [HOH=Y/N ]]
</source>
where:
* '''selection''' can be any existing or newly-defined selection
* '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
* '''HOH''' (default Y) allows to exclude (N) water residues from the list

= Examples =
<source lang="python">
PyMOL>listselection 1efa, output=P
Residues in '1efa': 1043
Results saved in listselection_1efa.txt
</source>

<source lang="python">
PyMOL>listselection sele, output=S, HOH=N
Residues in 'sele, without HOH': 7
1LBH/A/ARG/86
1LBH/A/ALA/87
1LBH/A/ASP/88
1LBH/A/GLN/89
1LBH/A/LEU/90
1LBH/A/GLY/91
1LBH/A/ALA/92
</source>

<source lang="python">
PyMOL>listselection 1efa and resn LEU, output=S
Residues in '1efa and resn LEU': 108
1efa/A/LEU/6
1efa/A/LEU/45
1efa/A/LEU/56
[...]
1efa/C/LEU/323
1efa/C/LEU/330
</source>

= Code =
Copy the following text and save it as listselection.py

<source lang="python">
from pymol import cmd, stored

def listselection (selection, output="N", HOH="Y"):
"""
usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]

More information at: PymolWiki: http://http://pymolwiki.org/index.php/ListSelection2
AUTHOR: Pietro Gatti-Lafranconi, 2013
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""
printedselection=""
extra=""
counter=0
sel=selection
objs=cmd.get_object_list(sel)

if HOH=="N":
sel=selection+" and not resn HOH"
extra=", without HOH"

for a in range(len(objs)):
m1=cmd.get_model(sel+" and "+objs[a])
for x in range(len(m1.atom)):
if m1.atom[x-1].resi!=m1.atom[x].resi:
printedselection+="%s/%s/%s/%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resn, m1.atom[x].resi)
counter+=1

print "Residues in '%s%s': %s" % (selection, extra, counter)
if output=="S": print printedselection
if output=="P":
f=open('listselection_'+selection+'.txt','w')
f.write("Residues in '%s%s': %s\n" % (selection, extra, counter))
f.write(printedselection)
f.close()
print "Results saved in listselection_%s.txt" % selection

cmd.extend('listselection',listselection)
</source>
[[Category:Script_Library|List Selection]]
[[Category:ObjSel_Scripts]]

ListSelection2

2013-03-14T15:42:17Z

PietroGattiLafranconi:

= Overview =
Alternative script to [[List_Selection]] that will:
* list multiple residues once
* include water and hetatoms
* account for different chains/objects
* produce a screen/printed output

= Usage =
<source lang="python">
listselection selection, [output=N/S/P, [HOH=Y/N ]]
</source>
where:
* '''selection''' can be any existing or newly-defined selection
* '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
* '''HOH''' (default Y) allows to exclude (N) water residues from the list

= Examples =
<source lang="python">
PyMOL>listselection 1efa, output=P
Residues in '1efa': 1043
Results saved in listselection_1efa.txt
</source>

<source lang="python">
PyMOL>listselection sele, output=S, HOH=N
Residues in 'sele, without HOH': 5
2P9H\A\101\ARG
2P9H\A\102\SER
2P9H\A\103\GLY
2P9H\A\104\VAL
2P9H\A\105\GLU
</source>

<source lang="python">
PyMOL>listselection 1efa and resn LEU, output=S
Residues in '1EFA and resn LEU': 108
1efa\A\6\LEU
1efa\A\45\LEU
[...]
1efa\C\323\LEU
1efa\C\330\LEU
</source>

= Code =
Copy the following text and save it as listselection.py

<source lang="python">
from pymol import cmd, stored

def listselection (selection, output="N", HOH="Y"):
"""
usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]

More information at: PymolWiki: http://http://pymolwiki.org/index.php/ListSelection2
AUTHOR: Pietro Gatti-Lafranconi, 2013
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""
printedselection=""
extra=""
counter=0
sel=selection
objs=cmd.get_object_list(sel)

if HOH=="N":
sel=selection+" and not resn HOH"
extra=", without HOH"

for a in range(len(objs)):
m1=cmd.get_model(sel+" and "+objs[a])
for x in range(len(m1.atom)):
if m1.atom[x-1].resi!=m1.atom[x].resi:
printedselection+="%s/%s/%s/%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resn, m1.atom[x].resi)
counter+=1

print "Residues in '%s%s': %s" % (selection, extra, counter)
if output=="S": print printedselection
if output=="P":
f=open('listselection_'+selection+'.txt','w')
f.write("Residues in '%s%s': %s\n" % (selection, extra, counter))
f.write(printedselection)
f.close()
print "Results saved in listselection_%s.txt" % selection

cmd.extend('listselection',listselection)
</source>
[[Category:Script_Library|List Selection]]
[[Category:ObjSel_Scripts]]

ListSelection2

2013-03-14T10:49:30Z

PietroGattiLafranconi:

= Overview =
Alternative script to [[List_Selection]] that will:
* list multiple residues once
* include water and hetatoms
* account for different chains/objects
* produce a screen/printed output

= Usage =
<source lang="python">
listselection selection, [output=N/S/P, [HOH=Y/N ]]
</source>
where:
* '''selection''' can be any existing or newly-defined selection
* '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
* '''HOH''' (default Y) allows to exclude (N) water residues from the list

= Examples =
<source lang="python">
PyMOL>listselection 1efa, output=P
Residues in '1efa': 1043
Results saved in listselection_1efa.txt
</source>

<source lang="python">
PyMOL>listselection sele, output=S, HOH=N
Residues in 'sele, without HOH': 5
2P9H\A\101\ARG
2P9H\A\102\SER
2P9H\A\103\GLY
2P9H\A\104\VAL
2P9H\A\105\GLU
</source>

<source lang="python">
PyMOL>listselection 1efa and resn LEU, output=S
Residues in '1EFA and resn LEU': 108
1efa\A\6\LEU
1efa\A\45\LEU
[...]
1efa\C\323\LEU
1efa\C\330\LEU
</source>

= Code =
Copy the following text and save it as listselection.py

<source lang="python">
from pymol import cmd, stored

def listselection (selection, output="N", HOH="Y"):
"""
usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]

More information at: PymolWiki: http://http://pymolwiki.org/index.php/ListSelection2
AUTHOR: Pietro Gatti-Lafranconi, 2013
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""
printedselection=""
extra=""
counter=0
sel=selection
objs=cmd.get_object_list(sel)

if HOH=="N":
sel=selection+" and not resn HOH"
extra=", without HOH"

for a in range(len(objs)):
m1=cmd.get_model(sel+" and "+objs[a])
for x in range(len(m1.atom)):
if m1.atom[x-1].resi!=m1.atom[x].resi:
printedselection+="%s\%s\%s\%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resi, m1.atom[x].resn)
counter+=1

print "Residues in '%s%s': %s" % (selection, extra, counter)
if output=="S": print printedselection
if output=="P":
f=open('listselection_'+selection+'.txt','w')
f.write("Residues in '%s%s': %s\n" % (selection, extra, counter))
f.write(printedselection)
f.close()
print "Results saved in listselection_%s.txt" % selection

cmd.extend('listselection',listselection)
</source>
[[Category:Script_Library|List Selection]]
[[Category:ObjSel_Scripts]]

ListSelection2

2013-03-14T10:42:14Z

PietroGattiLafranconi: small code update

= Overview =
Alternative script to [[List_Selection]] that will:
* list multiple residues once
* include water and hetatoms
* account for different chains/objects
* produce a screen/printed output

= Usage =
<source lang="python">
listselection selection, [output=N/S/P, [HOH=Y/N ]]
</source>
where:
* '''selection''' can be any existing or newly-defined selection
* '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
* '''HOH''' (default Y) allows to exclude (N) water residues from the list

= Examples =
<source lang="python">
PyMOL>listselection 1efa, output=P
Residues in '1efa': 1043
Results saved in listselection_1efa.txt
</source>

<source lang="python">
PyMOL>listselection sele, output=S, HOH=N
Residues in 'sele, without HOH': 5
2P9H\A\101\ARG
2P9H\A\102\SER
2P9H\A\103\GLY
2P9H\A\104\VAL
2P9H\A\105\GLU
</source>

<source lang="python">
PyMOL>listselection 1efa and resn LEU, output=S
Residues in '1EFA and resn LEU': 108
1efa\A\6\LEU
1efa\A\45\LEU
[...]
1efa\C\323\LEU
1efa\C\330\LEU
</source>

= Code =
Copy the following text and save it as listselection.py

<source lang="python">
from pymol import cmd, stored

def listselection (selection, output="N", HOH="Y"):
"""
usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]
"""
printedselection=""
extra=""
counter=0
sel=selection
objs=cmd.get_object_list(sel)

if HOH=="N":
sel=selection+" and not resn HOH"
extra=", without HOH"

for a in range(len(objs)):
m1=cmd.get_model(sel+" and "+objs[a])
for x in range(len(m1.atom)):
if m1.atom[x-1].resi!=m1.atom[x].resi:
printedselection+="%s\%s\%s\%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resi, m1.atom[x].resn)
counter+=1

print "Residues in '%s%s': %s" % (selection, extra, counter)
if output=="S": print printedselection
if output=="P":
f=open('listselection_'+selection+'.txt','w')
f.write("Residues in '%s%s': %s\n" % (selection, extra, counter))
f.write(printedselection)
f.close()
print "Results saved in listselection_%s.txt" % selection

cmd.extend('listselection',listselection)
</source>
[[Category:Script_Library|List Selection]]
[[Category:ObjSel_Scripts]]

ListSelection2

2013-03-13T17:39:30Z

PietroGattiLafranconi: small script to list the content of pymol selections

DistancesRH

2013-01-13T15:39:01Z

PietroGattiLafranconi:

{{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]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==
distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

== Required Arguments ==
* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
'''example #1'''
<source lang="python">
distancesRH 2WHH, 25, 3.2, show=Y
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen (figure 1, left).
<source lang="python">
distancesRH 2WHH, 25, 3.2, show=Y, aname=OD1, output=P
</source>
Same result as before, but only distances from atom OD1 are measured and shown. Results will be printed in 'distancesRH_25-OD1.txt' (figure 1, right).

[[File:distancesRH_ex1.png|450px|example #1]]

'''example #2'''
<source lang="python">
distancesRH 1EFA, 901, 3.5, show=Y
</source>
Will show distances between all atoms in resi 901 of 1EFA and all atoms within 3.5 Å (figure 2, left).
<source lang="python">
distancesRH 1EFA, 901, 3.5, show=Y, Hbonds=Y
</source>
Distances will now be calculated between atoms that can form H bonds only (figure 2, right).

[[File:distancesRH_ex2.png|450px|example #2]]

'''example #3'''
<source lang="python">
distancesRH 1EFA, 18, 4.7, chain=B, show=Y, aname=NE2
</source>
Distances between atom NE2 of residue 19 in chain B of 1EFA and all atoms within 4.7 Å (all of which are in the DNA fragment of chain D, figure 3).

[[File:distancesRH_ex3.png|300px|example #3]]

== Notes, Further Developments and Requests ==
* This script works with visible objects (handling of multiple states will hopefully be implemented soon)
* As it is intended to be user-friendly more than fast, this script is not suitable to calculate distances between large objects. Use [[Quick_dist]] instead.

== Updates ==
* '''11/01/2013''' - edit #1: ''distances measured between different chains''
* '''13/01/2013''' - edit #2: ''print output optimsed''

== The Code ==

Copy the following text and save it as distancesRH.py

<source lang="python">

"""
DESCRIPTION
Given an object, a reference amino acid and a radius, this scripts calculates pairwise
distances between all atoms in the reference and all atoms that fall within the given range.
Distances are either returned on screen (default) or printed on file.
Distances can be calculated from a single atom only.
Optionally, only atoms that can form H-bonds can be returned (but check distances!)

More information at: PymolWiki
http://pymolwiki.org/index.php/DistancesRH

AUTHOR
Pietro Gatti-Lafranconi, 2012
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+obj)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
if aname=="*": aname="ALL"
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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

DistancesRH

2013-01-13T15:38:17Z

PietroGattiLafranconi: graphical outputs

{{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]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==
distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

== Required Arguments ==
* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
'''example #1'''
<source lang="python">
distancesRH 2WHH, 25, 3.2, show=Y
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen (figure 1, left).
<source lang="python">
distancesRH 2WHH, 25, 3.2, show=Y, aname=OD1, output=P
</source>
Same result as before, but only distances from atom OD1 are measured and shown. Results will be printed in 'distancesRH_25-OD1.txt' (figure 1, right).

[[File:distancesRH_ex1.png|450px|example #1]]

'''example #2'''
<source lang="python">
distancesRH 1EFA, 901, 3.5, show=Y
</source>
Will show distances between all atoms in resi 901 of 1EFA and all atoms within 3.5 Å (figure 2, left).
<source lang="python">
distancesRH 1EFA, 901, 3.5, show=Y, Hbonds=Y
</source>
Distances will now be calculated between atoms that can form H bonds only (figure 2, right).

[[File:distancesRH_ex2.png|300px|example #2]]

'''example #3'''
<source lang="python">
distancesRH 1EFA, 18, 4.7, chain=B, show=Y, aname=NE2
</source>
Distances between atom NE2 of residue 19 in chain B of 1EFA and all atoms within 4.7 Å (all of which are in the DNA fragment of chain D, figure 3).

[[File:distancesRH_ex3.png|450px|example #3]]

== Notes, Further Developments and Requests ==
* This script works with visible objects (handling of multiple states will hopefully be implemented soon)
* As it is intended to be user-friendly more than fast, this script is not suitable to calculate distances between large objects. Use [[Quick_dist]] instead.

== Updates ==
* '''11/01/2013''' - edit #1: ''distances measured between different chains''
* '''13/01/2013''' - edit #2: ''print output optimsed''

== The Code ==

Copy the following text and save it as distancesRH.py

<source lang="python">

"""
DESCRIPTION
Given an object, a reference amino acid and a radius, this scripts calculates pairwise
distances between all atoms in the reference and all atoms that fall within the given range.
Distances are either returned on screen (default) or printed on file.
Distances can be calculated from a single atom only.
Optionally, only atoms that can form H-bonds can be returned (but check distances!)

More information at: PymolWiki
http://pymolwiki.org/index.php/DistancesRH

AUTHOR
Pietro Gatti-Lafranconi, 2012
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+obj)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
if aname=="*": aname="ALL"
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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

File:DistancesRH ex3.png

2013-01-13T15:17:12Z

PietroGattiLafranconi:

File:DistancesRH ex2.png

2013-01-13T15:16:59Z

PietroGattiLafranconi:

File:DistancesRH ex1.png

2013-01-13T15:16:35Z

PietroGattiLafranconi:

DistancesRH

2013-01-13T15:15:35Z

PietroGattiLafranconi: code update

{{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]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==
distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

== Required Arguments ==
* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
example #1
<source lang="python">
distancesRH 2WHH, 25, 3.2
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen.

example #2
<source lang="python">
distancesRH 1LVM, 151, 3, B, P, Y, Y, N
</source>
Will show distances between N of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.

== Notes, Further Developments and Requests ==
* This script works with visible objects (handling of multiple states will hopefully be implemented soon)
* As it is intended to be user-friendly more than fast, this script is not suitable to calculate distances between large objects. Use [[Quick_dist]] instead.

== Updates ==
* '''11/01/2013''' - edit #1: ''distances measured between different chains''
* '''13/01/2013''' - edit #2: ''print output optimsed''

== The Code ==

Copy the following text and save it as distancesRH.py

<source lang="python">

"""
DESCRIPTION
Given an object, a reference amino acid and a radius, this scripts calculates pairwise
distances between all atoms in the reference and all atoms that fall within the given range.
Distances are either returned on screen (default) or printed on file.
Distances can be calculated from a single atom only.
Optionally, only atoms that can form H-bonds can be returned (but check distances!)

More information at: PymolWiki
http://pymolwiki.org/index.php/DistancesRH

AUTHOR
Pietro Gatti-Lafranconi, 2012
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+obj)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
if aname=="*": aname="ALL"
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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

DistancesRH

2013-01-11T11:50:01Z

PietroGattiLafranconi:

{{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]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==
distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

== Required Arguments ==
* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
example #1
<source lang="python">
distancesRH 2WHH, 25, 3.2
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen.

example #2
<source lang="python">
distancesRH 1LVM, 151, 3, B, P, Y, Y, N
</source>
Will show distances between N of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.

== Notes, Further Developments and Requests ==
* This script works with visible objects (handling of multiple states will hopefully be implemented soon)
* As it is intended to be user-friendly more than fast, this script is not suitable to calculate distances between large objects. Use [[Quick_dist]] instead.

== Updates ==
* '''11/01/2013''' - edit #1: ''distances are now calculated across different chains as well''

== The Code ==

Copy the following text and save it as distancesRH.py

<source lang="python">

"""
DESCRIPTION
Given an object, a reference amino acid and a radius, this scripts calculates pairwise
distances between all atoms in the reference and all atoms that fall within the given range.
Distances are either returned on screen (default) or printed on file.
Distances can be calculated from a single atom only.
Optionally, only atoms that can form H-bonds can be returned (but check distances!)

More information at: PymolWiki
http://pymolwiki.org/index.php/DistancesRH

AUTHOR
Pietro Gatti-Lafranconi, 2012
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+obj)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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

DistancesRH

2013-01-11T11:49:25Z

PietroGattiLafranconi: code update

{{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]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==
distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

== Required Arguments ==
* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
example #1
<source lang="python">
distancesRH 2WHH, 25, 3.2
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen.

example #2
<source lang="python">
distancesRH 1LVM, 151, 3, B, P, Y, Y, N
</source>
Will show distances between N of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.

== Notes, Further Developments and Requests ==
* This script works with visible objects (handling of multiple states will hopefully be implemented soon)
* As it is intended to be user-friendly more than fast, this script is not suitable to calculate distances between large objects. Use [[Quick_dist]] instead.

== Updates ==
* ''11/01/2013'' - edit #1: '''distances are now calculated across different chains as well'''

== The Code ==

Copy the following text and save it as distancesRH.py

<source lang="python">

"""
DESCRIPTION
Given an object, a reference amino acid and a radius, this scripts calculates pairwise
distances between all atoms in the reference and all atoms that fall within the given range.
Distances are either returned on screen (default) or printed on file.
Distances can be calculated from a single atom only.
Optionally, only atoms that can form H-bonds can be returned (but check distances!)

More information at: PymolWiki
http://pymolwiki.org/index.php/DistancesRH

AUTHOR
Pietro Gatti-Lafranconi, 2012
Please inform me if you use/improve/like/dislike/publish with this script.
CC BY-NC-SA
"""

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+obj)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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

DistancesRH

2013-01-04T11:45:48Z

PietroGattiLafranconi:

{{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]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==
distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

== Required Arguments ==
* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
example #1
<source lang="python">
distancesRH 2WHH, 25, 3.2
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen.

example #2
<source lang="python">
distancesRH 1LVM, 151, 3, B, P, Y, Y, N
</source>
Will show distances between N of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.

== Notes, Further Developments and Requests ==
* This script works with visible objects
* As it is intended to be user-friendly more than fast, this script is not suitable to calculate distances between large objects. Use [[Quick_dist]] instead.
* '''request #1''': a version that handles multiple states

== The Code ==
<source lang="python">

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+cen)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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

User:PietroGattiLafranconi

2013-01-03T14:10:29Z

PietroGattiLafranconi:

* Is new to PyMOLWiki
* Recently submitted [[DistancesRH]]
* Will be happy to receive feedbacks/suggestions
* Wonders if [[DistancesRH]] is worth uploading in [[Pymol-script-repo]]
* can be found [http://www.bio.cam.ac.uk/~fhlab/members/pg356.shtml here]

User:PietroGattiLafranconi

2013-01-02T16:37:13Z

PietroGattiLafranconi: Created page with "* Is new to PyMOLWiki * Recently submitted DistancesRH * Will be happy to receive feedbacks/suggestions * Wonders if DistancesRH is worth uploading in Pymol-script-repo"

* Is new to PyMOLWiki
* Recently submitted [[DistancesRH]]
* Will be happy to receive feedbacks/suggestions
* Wonders if [[DistancesRH]] is worth uploading in [[Pymol-script-repo]]

DistancesRH

2013-01-02T16:32:05Z

PietroGattiLafranconi:

{{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]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==

distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

'''Note #1:''' the selected molecule must be visible.

'''Note #2:''' soon a version that handles multiple states.

== Required Arguments ==

* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
example #1
<source lang="python">
distancesRH 2WHH, 25, 3.2
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen.

example #2
<source lang="python">
distancesRH 1LVM, 151, 3, B, P, Y, Y, N
</source>
Will show distances between CB of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.

== The Code ==
<source lang="python">

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+cen)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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

DistancesRH

2013-01-02T16:31:19Z

PietroGattiLafranconi: 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]
}}

== Introduction ==
Given an object, a reference amino acid and a radius, this scripts calculates pairwise distances between atom(s) in the reference and all atoms that fall within the given range.

The script is intended to provide a range of useful tools while requiring minimal coding skills (i.e. it is not optimised for efficiency).

By changing input parameters it is possible to:
* choose the output (none, on screen, on file)
* measure distances from one single atom
* display distance objects in pymol
* restrict distances between hydrogen-bond forming atoms only

The script also runs a number of controls to verify that inputs and outputs exists/are suitable.

== Usage ==

distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

'''Note #1:''' the selected molecule must be visible.
'''Note #2:''' soon a version that manages multiple states.

== Required Arguments ==

* '''obj''' = object name
* '''ref''' = reference amino acid id
* '''dist''' = radius in Angstroms

== Optional Arguments ==
* ''chain'' = selected chain
* ''output'' = accepts S (screen), P (print) or N (none), default=S
* ''show'' = shows distances in pymol window, default=N
* ''Hbonds'' = restricts results to atoms that can form Hbonds, default=N
* ''aname'' = selects a specific atom in reference object and to calculate distances from one individual atom

== Examples ==
example #1
<source lang="python">
distancesRH 2WHH, 25, 3.2
</source>
Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen.

example #2
<source lang="python">
distancesRH 1LVM, 151, 3, B, P, Y, Y, N
</source>
Will show distances between CB of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.

== The Code ==
<source lang="python">

from pymol import cmd, stored, math

def distancesRH (obj, ref, dist, chain=0, output="S", show="N", Hbonds="N", aname="*"):
"""
usage: distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]

obj: object name, ref:reference aa, dist: radius in A, chain: selected chain
output: accepts S (screen), P (print) or N (none), default=S
show: shows distances in pymol window, default=N
Hbonds: restricts results to atoms that can form Hbonds, default=N
aname: name of a specific atom in ref (to calculate distances from one atom only)

example: distancesRH 2WHH, 25, 3.2, [B, [S, [N, [Y, [CB]]]]]
"""
print ""
#delete previous selections and displayed distances
cmd.delete ("dist*")
cmd.delete ("Atoms")
cmd.delete ("Residues")
cmd.delete ("Reference")
cmd.delete ("Hbonds")
cmd.delete ("RefAtom")
#creates and names selections
if chain==0: cen=obj
else: cen=obj+" and chain "+chain
refA=" and resi "+ref+" and name "+aname
cmd.select("Reference", "byres "+cen+refA)
m1=cmd.get_model ("Reference")
if aname!="*":
cmd.select("RefAtom", cen+refA)
m1=cmd.get_model ("RefAtom")
cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+cen)
cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
cmd.select("Residues", "byres Atoms")
m2=cmd.get_model("Atoms and visible")
if Hbonds=="Y":
cmd.select("__Hbonds1", "Reference and not symbol c")
if aname!="*":
cmd.select("__Hbonds1", "RefAtom and not symbol c")
cmd.select("__Hbonds2", "Atoms and not symbol c")
cmd.select("Hbonds", "__Hbonds1 or __Hbonds2")
cmd.show("lines", "Hbonds")
m1=cmd.get_model ("__Hbonds1")
m2=cmd.get_model ("__Hbonds2 and visible")

#controllers
if (not (output=="S" or output=="N" or output=="P")) or (not (show=="Y" or show=="N")) or (not (Hbonds=="Y" or Hbonds=="N")):
print "Malformed input, please try again"
return
abort=1
abort2=0
mc=cmd.get_model(cen)
for c0 in range(len(mc.atom)):
if mc.atom[c0].resi==ref: abort=0
mc2=cmd.get_model(cen+refA)
if aname!="*":
abort2=1
for c00 in range (len(mc2.atom)):
if mc2.atom[c00].name==aname: abort2=0
if Hbonds=="Y":
if aname[0]=="C":
print "Warning: no atoms in the selection can form H-bonds"
return
if abort==1: print "Warning: no such residue in the reference object"
if abort2==1:
if abort==0: print "Warning: no such atom in the reference object"
if abort==1 or abort2==1: return

#measures distances
distance2=[]
distances=[]
screenOP=""
fileOP=""
for c1 in range(len(m1.atom)):
for c2 in range(len(m2.atom)):
if math.sqrt(sum(map(lambda f: (f[0]-f[1])**2, zip(m1.atom[c1].coord,m2.atom[c2].coord))))<float(dist):
distance=cmd.distance (obj+"//"+m1.atom[c1].chain+"/"+m1.atom[c1].resi+"/"+m1.atom[c1].name, obj+"//"+m2.atom[c2].chain+"/"+m2.atom[c2].resi+"/"+m2.atom[c2].name)
distances.append(distance)
screenOP+="%s/%s/%s/%s to %s/%s/%s/%s: %.3f\n" % (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
fileOP+="%s/%s/%s/%s\t\t\t%s/%s/%s/%s\t\t\t\t%.5f\n"% (m1.atom[c1].chain,m1.atom[c1].resn,m1.atom[c1].resi,m1.atom[c1].name,m2.atom[c2].chain,m2.atom[c2].resn,m2.atom[c2].resi,m2.atom[c2].name, distance)
#last controller
if len(distances)==0:
if abort2==0:
print "Warning: no atoms within the selected range"
return

#data outputs
if output=="N": print "Data recorded, but not printed"
if output=="S":
print "Distance of atoms in "+obj+"/"+ref+"/"+aname+" to all atoms within "+dist+" Angstroms"
if Hbonds=="Y": print "Distances restricted to potential H-bond pairs"
print screenOP
if output=="P":
print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
f=open('distances_rH_'+ref+'-'+aname+'.txt','w')
f.write("Pairwise distances betweet atoms in %s and all atoms within %s Angstroms\n" % (obj+"/"+ref+"/"+aname, dist))
if Hbonds=="Y": f.write("Distances restricted to potential H-bond pairs\n")
f.write("Atom in reference\tAtom in destination\t\tdistance\n")
f.write(fileOP)
f.close()
print "All done! Good luck with your data"

#graphical output
if show=="N": cmd.delete ("dist*")
if show=="Y":
cmd.show("lines", "Reference")
cmd.show("lines", "Residues")

cmd.extend("distancesRH", distancesRH);
</source>

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