PyMOL Wiki - User contributions [en]

Helicity check

2007-04-20T18:52:23Z

Avelldiroll:

helicity_check show the evolution of O - N distances over an amino acid sequence

See for further info:

Protein Sci ROHL and DOIG 5 (8) 1687

"Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides."

uses:
*in the pymol console:
>run pymol_helicity_check.py
----> select some consecutive amino acids
- this is nicely done with the Display->Sequence tool
>helicity_check()
*installing helicity_check
copy pymol_helicity_check.py in $PYMOL_INSTALL_DIR/modules/pmg_tk/startup
launch Pymol: you now have a new option in the Plugin menu

helicity_check uses gnuplot (http://www.gnuplot.info) to display its results.
As a consequence gnuplot needs to be installed.

This plugin was tested on linux only, it might need some modifications to run on
other OSes. (hints: launching gnuplot and path to dumpfile)

<source lang="python">
# pymol_helicity_check.py
# Copyright (c) 2006-2007 Julien Lefeuvre <lefeuvrejulien@yahoo.fr>
#

"""
Pymol plugin for checking helicity type

helicity_check() takes as input a selection ('sele' by default)
of at least 5 amino acids and computes the distances between
O(i) - N(i+3)
O(i) - N(i+4)
O(i) - N(i+5)
See for further info:
Protein Sci ROHL and DOIG 5 (8) 1687
'Models for the 3(10)-helix/coil, pi-helix/coil,
and alpha-helix/3(10)-helix/coil transitions in isolated peptides.'

uses:
*in the pymol console:
>run pymol_helicity_check.py
----> select some consecutive amino acids
- this is nicely done with the Display->Sequence tool
>helicity_check()
*installing helicity_check
copy pymol_helicity_check.py in $PYMOL_INSTALL_DIR/modules/pmg_tk/startup
launch Pymol: you now have a new option in the Plugin menu

helicity_check uses gnuplot (http://www.gnuplot.info) to display its results
As a consequence gnuplot needs to be installed.

This plugin was tested on linux only, it my need some modifications to run on
other OSes (hints: launching gnuplot and path to dumpfile)
"""

__author__ = "Julien Lefeuvre <lefeuvrejulien@yahoo.fr>"
__version__ = "1.0"
__date__ = "2007-04-02"
__copyright__ = "Copyright (c) 2007 %s. All rights reserved." % __author__
__licence__ = "BSD"

from pymol import cmd
from math import sqrt
import sys
import os
import subprocess
import time

def __init__(self):
"""init function in order to have a nice menu option in Pymol"""
self.menuBar.addmenuitem('Plugin', 'command', 'Helicity Check',
label='Helicity Check', command = lambda: helicity_check())

class Residue(object):

def __init__(self):
self.name=None
self.index=None
self.Ocoord=None
self.Ncoord=None

def calc_distON(Ocoord,Ncoord):
"""return the distance between 2 atoms given their coordinates"""
sum = 0
for o, n in zip(Ocoord, Ncoord):
sum += (o - n)**2
return sqrt(sum)

def helicity_check(selection='sele'):
"""calcultate distance O[res i]-N[res i+3]
O[res i]-N[res i+4]
O[res i]-N[res i+5]
"""
seq_model = cmd.get_model(selection) #get info from selection
res_lim = seq_model.get_residues()

if len(res_lim)<5:
sys.stderr.write("\nPlease select at least 5 residues\n")
return

atom_list = seq_model.atom
res_data=[]

for start,end in res_lim: #extract the data we are interested in
res=Residue()
for atom in atom_list[start:end]:
if atom.name == 'N':
res.name = atom.resn
res.index = atom.resi
res.Ncoord = atom.coord
elif atom.name == 'O':
res.Ocoord = atom.coord
if res.Ocoord and res.Ncoord and res.name and res.index:
res_data.append(res)
else:
sys.stderr.write("\nPlease select complete protein residues\n")
return

res_list = [int(res.index) for res in res_data]

if res_list != range(res_list[0], res_list[-1]+1):
sys.stderr.write("\nPlease select a unbrocken residue sequence\n")
return

distON3 = []
distON4 = []
distON5 = []
distONs = [distON3, distON4, distON5]

for i,res in enumerate(res_data[:-5]): #distances calculations
resis = res_data[i+3:i+6]
for resi, distONi in zip(resis, distONs):
distONi.append(calc_distON(res.Ocoord, resi.Ncoord))

dump = os.tmpnam()+'.dat'
dumpfile = file(dump, 'w')

sys.stdout.write('\n#Distances O(i)---N(i+n)\n'
'#ResNum , d(O(i)-N(i+3)) , d(O(i)-N(i+4)) , d(O(i)-N(i+4))\n')
for i, d3, d4, d5 in zip(res_list, distON3, distON4, distON5):
#writing console output
sys.stdout.write(
' %i , %f , %f , %f \n'%(i, d3, d4, d5))
#writing data to a dump file for use by gnuplot
dumpfile.write(
' %i %f %f %f \n'%(i, d3, d4, d5))
dumpfile.flush()

#launch a gnuplot window to show the distances
gnuplotcmd = subprocess.Popen(['/usr/bin/gnuplot'], shell=True,
stdin=subprocess.PIPE)
gnuplotcmd.stdin.write('set autoscale\n')
gnuplotcmd.stdin.write("plot "
"'%s' using 1:2 title 'd(O(i)-N(i+3))' with lines, "
"'%s' using 1:3 title 'd(O(i)-N(i+4))' with lines, "
"'%s' using 1:4 title 'd(O(i)-N(i+5))' with lines\n'"
% (dump, dump, dump))
time.sleep(3)
dumpfile.close()
os.remove(dump)
</source>

User:Avelldiroll

2007-04-03T14:05:29Z

Avelldiroll: New page: Julien Lefeuvre PhD Student Institut Européen de Chimie et de Biologie (IECB) UMR 5248 CBMN, Chimie et Biologie des Membranes et des Nanoobjets, CNRS-Universite Bordeaux...

Julien Lefeuvre 
PhD Student 

Institut Européen de Chimie et de Biologie (IECB) 
UMR 5248 CBMN, Chimie et Biologie des Membranes et des Nanoobjets, 
CNRS-Universite Bordeaux 1-ENITAB 
2, rue Robert Escarpit - 33607 Pessac Cedex - France 
Tél. : 33 (0)5 40 00 30 31 
Fax. : 33 (0)5 40 00 30 73 
http://www.iecb.u-bordeaux.fr

Helicity check

2007-04-03T12:44:51Z

Avelldiroll: update to improve portability

helicity_check show the evolution of O - N distances over an amino acid sequence

See for further info:

Protein Sci ROHL and DOIG 5 (8) 1687

"Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides."

uses:
*in the pymol console:
>run pymol_helicity_check.py
----> select some consecutive amino acids
- this is nicely done with the Display->Sequence tool
>helicity_check()
*installing helicity_check
copy pymol_helicity_check.py in $PYMOL_INSTALL_DIR/modules/pmg_tk/startup
launch Pymol: you now have a new option in the Plugin menu

helicity_check uses gnuplot (http://www.gnuplot.info) to display its results.
As a consequence gnuplot needs to be installed.

This plugin was tested on linux only, it my need some modifications to run on
other OSes. (hints: launching gnuplot and path to dumpfile)

<source lang="python">
# pymol_helicity_check.py
# Copyright (c) 2006-2007 Julien Lefeuvre <lefeuvrejulien@yahoo.fr>
#

"""
Pymol plugin for checking helicity type

helicity_check() takes as input a selection ('sele' by default)
of at least 5 amino acids and computes the distances between
O(i) - N(i+3)
O(i) - N(i+4)
O(i) - N(i+5)
See for further info:
Protein Sci ROHL and DOIG 5 (8) 1687
'Models for the 3(10)-helix/coil, pi-helix/coil,
and alpha-helix/3(10)-helix/coil transitions in isolated peptides.'

uses:
*in the pymol console:
>run pymol_helicity_check.py
----> select some consecutive amino acids
- this is nicely done with the Display->Sequence tool
>helicity_check()
*installing helicity_check
copy pymol_helicity_check.py in $PYMOL_INSTALL_DIR/modules/pmg_tk/startup
launch Pymol: you now have a new option in the Plugin menu

helicity_check uses gnuplot (http://www.gnuplot.info) to display its results
As a consequence gnuplot needs to be installed.

This plugin was tested on linux only, it my need some modifications to run on
other OSes (hints: launching gnuplot and path to dumpfile)
"""

__author__ = "Julien Lefeuvre <lefeuvrejulien@yahoo.fr>"
__version__ = "1.0"
__date__ = "2007-04-02"
__copyright__ = "Copyright (c) 2007 %s. All rights reserved." % __author__
__licence__ = "BSD"

from pymol import cmd
from math import sqrt
import sys
import os
import subprocess
import time

def __init__(self):
"""init function in order to have a nice menu option in Pymol"""
self.menuBar.addmenuitem('Plugin', 'command', 'Helicity Check',
label='Helicity Check', command = lambda: helicity_check())

class Residue(object):

def __init__(self):
self.name=None
self.index=None
self.Ocoord=None
self.Ncoord=None

def calc_distON(Ocoord,Ncoord):
"""return the distance between 2 atoms given their coordinates"""
sum = 0
for o, n in zip(Ocoord, Ncoord):
sum += (o - n)**2
return sqrt(sum)

def helicity_check(selection='sele'):
"""calcultate distance O[res i]-N[res i+3]
O[res i]-N[res i+4]
O[res i]-N[res i+5]
"""
seq_model = cmd.get_model(selection) #get info from selection
res_lim = seq_model.get_residues()

if len(res_lim)<5:
sys.stderr.write("\nPlease select at least 5 residues\n")
return

atom_list = seq_model.atom
res_data=[]

for start,end in res_lim: #extract the data we are interested in
res=Residue()
for atom in atom_list[start:end]:
if atom.name == 'N':
res.name = atom.resn
res.index = atom.resi
res.Ncoord = atom.coord
elif atom.name == 'O':
res.Ocoord = atom.coord
if res.Ocoord and res.Ncoord and res.name and res.index:
res_data.append(res)
else:
sys.stderr.write("\nPlease select complete protein residues\n")
return

res_list = [int(res.index) for res in res_data]

if res_list != range(res_list[0], res_list[-1]+1):
sys.stderr.write("\nPlease select a unbrocken residue sequence\n")
return

distON3 = []
distON4 = []
distON5 = []
distONs = [distON3, distON4, distON5]

for i,res in enumerate(res_data[:-5]): #distances calculations
resis = res_data[i+3:i+6]
for resi, distONi in zip(resis, distONs):
distONi.append(calc_distON(res.Ocoord, resi.Ncoord))

dump = os.tmpnam()+'.dat'
dumpfile = file(dump, 'w')

sys.stdout.write('\n#Distances O(i)---N(i+n)\n'
'#ResNum , d(O(i)-N(i+3)) , d(O(i)-N(i+4)) , d(O(i)-N(i+4))\n')
for i, d3, d4, d5 in zip(res_list, distON3, distON4, distON5):
#writing console output
sys.stdout.write(
' %i , %f , %f , %f \n'%(i, d3, d4, d5))
#writing data to a dump file for use by gnuplot
dumpfile.write(
' %i %f %f %f \n'%(i, d3, d4, d5))
dumpfile.flush()

#launch a gnuplot window to show the distances
gnuplotcmd = subprocess.Popen(['/usr/bin/gnuplot'], shell=True,
stdin=subprocess.PIPE)
gnuplotcmd.stdin.write('set autoscale\n')
gnuplotcmd.stdin.write("plot "
"'%s' using 1:2 title 'd(O(i)-N(i+3))' with lines, "
"'%s' using 1:3 title 'd(O(i)-N(i+4))' with lines, "
"'%s' using 1:4 title 'd(O(i)-N(i+5))' with lines\n'"
% (dump, dump, dump))
time.sleep(3)
dumpfile.close()
os.remove(dump)
</source>

Category:Script Library

2007-04-02T20:32:51Z

Avelldiroll: added helicity_check

* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.

* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.

* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.

* [[Process_All_Files_In_Directory]] -- Do something to all files in a directory. The examples show how to print the disulfide bond lengths, then in general all sulfur distances (not necessarily bound).

* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)

* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''

* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

* [[grepsel]] -- Make named selections using regular expressions (protein sequence).

* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.

* [[Plane Wizard]] -- Wizard to draw planes between three picked points.

* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.

* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence

[[Category:Scripting|Script Library]]

Helicity check

2007-04-02T20:25:49Z

Avelldiroll: helicity_check show the evolution of O - N distances over an amino acid sequence

helicity_check show the evolution of O - N distances over an amino acid sequence

See for further info:

Protein Sci ROHL and DOIG 5 (8) 1687

"Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides."

uses:
*in the pymol console:
>run pymol_helicity_check.py
----> select some consecutive amino acids
- this is nicely done with the Display->Sequence tool
>helicity_check()
*installing helicity_check
copy pymol_helicity_check.py in $PYMOL_INSTALL_DIR/modules/pmg_tk/startup
launch Pymol: you now have a new option in the Plugin menu

helicity_check uses gnuplot (http://www.gnuplot.info) to display its results.
As a consequence gnuplot needs to be installed.

This plugin was tested on linux only, it my need some modifications to run on
other OSes. (hints: launching gnuplot and path to dumpfile)

<source lang="python">
# pymol_helicity_check.py
# Copyright (c) 2006-2007 Julien Lefeuvre <lefeuvrejulien@yahoo.fr>
#

"""
Pymol plugin for checking helicity type

helicity_check() takes as input a selection ('sele' by default)
of at least 5 amino acids and computes the distances between
O(i) - N(i+3)
O(i) - N(i+4)
O(i) - N(i+5)
See for further info:
Protein Sci ROHL and DOIG 5 (8) 1687
'Models for the 3(10)-helix/coil, pi-helix/coil,
and alpha-helix/3(10)-helix/coil transitions in isolated peptides.'

uses:
*in the pymol console:
>run pymol_helicity_check.py
----> select some consecutive amino acids
- this is nicely done with the Display->Sequence tool
>helicity_check()
*installing helicity_check
copy pymol_helicity_check.py in $PYMOL_INSTALL_DIR/modules/pmg_tk/startup
launch Pymol: you now have a new option in the Plugin menu

helicity_check uses gnuplot (http://www.gnuplot.info) to display its results
As a consequence gnuplot needs to be installed.

This plugin was tested on linux only, it my need some modifications to run on
other OSes (hints: launching gnuplot and path to dumpfile)
"""

__author__ = "Julien Lefeuvre <lefeuvrejulien@yahoo.fr>"
__version__ = "1.0"
__date__ = "2007-04-02"
__copyright__ = "Copyright (c) 2007 %s. All rights reserved." % __author__
__licence__ = "BSD"

from pymol import cmd
from math import sqrt
import sys
import subprocess

def __init__(self):
"""init function in order to have a nice menu option in Pymol"""
self.menuBar.addmenuitem('Plugin', 'command', 'Helicity Check',
label='Helicity Check', command = lambda: helicity_check())

class Residue(object):

def __init__(self):
self.name=None
self.index=None
self.Ocoord=None
self.Ncoord=None

def calc_distON(Ocoord,Ncoord):
"""return the distance between 2 atoms given their coordinates"""
sum = 0
for o, n in zip(Ocoord, Ncoord):
sum += (o - n)**2
return sqrt(sum)

def helicity_check(selection='sele'):
"""calcultate distance O[res i]-N[res i+3]
O[res i]-N[res i+4]
O[res i]-N[res i+5]
"""
seq_model = cmd.get_model(selection) #get info from selection
res_lim = seq_model.get_residues()

if len(res_lim)<5:
sys.stderr.write("\nPlease select at least 5 residues\n")
return

atom_list = seq_model.atom
res_data=[]

for start,end in res_lim: #extract the data we are interested in
res=Residue()
for atom in atom_list[start:end]:
if atom.name == 'N':
res.name = atom.resn
res.index = atom.resi
res.Ncoord = atom.coord
elif atom.name == 'O':
res.Ocoord = atom.coord
if res.Ocoord and res.Ncoord and res.name and res.index:
res_data.append(res)
else:
sys.stderr.write("\nPlease select complete protein residues\n")
return

res_list = [int(res.index) for res in res_data]

if res_list != range(res_list[0], res_list[-1]+1):
sys.stderr.write("\nPlease select a unbrocken residue sequence\n")
return

distON3 = []
distON4 = []
distON5 = []
distONs = [distON3, distON4, distON5]

for i,res in enumerate(res_data[:-5]): #distances calculations
resis = res_data[i+3:i+6]
for resi, distONi in zip(resis, distONs):
distONi.append(calc_distON(res.Ocoord, resi.Ncoord))

dump = '/tmp/helixdists.tmp'
dumpfile = file(dump,'w')

sys.stdout.write('\n#Distances O(i)---N(i+n)\n'
'#ResNum , d(O(i)-N(i+3)) , d(O(i)-N(i+4)) , d(O(i)-N(i+4))\n')
for i, d3, d4, d5 in zip(res_list, distON3, distON4, distON5):
#writing console output
sys.stdout.write(
' %i , %f , %f , %f \n'%(i, d3, d4, d5))
#writing data to a dump file for use by gnuplot
dumpfile.write(
' %i %f %f %f \n'%(i, d3, d4, d5))

#launch a gnuplot window to show the distances
gnuplotcmd = subprocess.Popen(['/usr/bin/gnuplot'], shell=True,
stdin=subprocess.PIPE)
gnuplotcmd.stdin.write('set autoscale\n')
gnuplotcmd.stdin.write("plot "
"'%s' using 1:2 title 'd(O(i)-N(i+3))' with lines, "
"'%s' using 1:3 title 'd(O(i)-N(i+4))' with lines, "
"'%s' using 1:4 title 'd(O(i)-N(i+5))' with lines\n'"
% (dump, dump, dump))
</source>