CreateSecondaryStructure - Revision history

Pyadmin: 9 revisions

2014-03-28T01:43:40Z

9 revisions

Newacct at 08:14, 27 November 2009

2009-11-27T08:14:15Z

New page

===DESCRIPTION===
To build a peptide sequence.

===SETUP===
run CreateSecondaryStructure.py

===NOTES / STATUS===
*Tested on Pymolv1.0, Windows platform
*Many bugs to be found

===USAGE===
*seqInfo = getTableFromCsvFile("seqInfo.csv")
with in the file something like:
MET,-54,-47
PRO,-54,-47

*seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
*createPeptide(seqInfo)

===EXAMPLES===
seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
createPeptide(seqInfo)

===SCRIPTS (CreateSecondaryStructures.py)===
CreateSecondaryStructures.py
<source lang="python">
##############################################
# Original Author: Dan Kulp
# Date : 9/8/2005
# MOdified by Jurgen F. Doreleijers
# For Hamid Eghbalnia
#
#############################################
# Call in window like :
# @C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils\CreateSecondaryStructures.py
# Next line is a pymol directive
python
import urllib

# Well I guess one can build a protein with it but the vdw contacts would be horrible.
# Peptide needs to be at least 2 residues.
def createPeptide(seqInfo):
cmd.delete("all")
# Creates residue TWO
editor.attach_amino_acid('pk1',seqInfo[1][0])
# Creates residue ONE
createSS('resi 2', sequence=seqInfo[0][0],terminal='N')
print "found sequence info for number of residues: ", len(seqInfo)
for i in range(2,len(seqInfo) ):
# resn is the residue number of the new residue
resn = i + 1
print "Adding residue: ", resn, seqInfo[i][0]
# Note that the previous residue is numbered i.
resi = 'resi '+`i`
createSS(resi, sequence=seqInfo[i][0])
for i in range( len(seqInfo) ):
resi = 'resi '+`i+1`
# print "Setting backbone angles for residue: ", (i+1), seqInfo[i][0],seqInfo[i][1],seqInfo[i][2]
set_phipsi(resi,seqInfo[i][1],seqInfo[i][2])

# Create generic secondary structure, based off a selection
def createSS(sel, sequence='ALA',repeat=1,terminal='C'):

# Set selection
selection = "%s and name %s" % (sel,terminal)

# Pick atom for editing - interestingly only need to do this for the first addition
cmd.edit(selection,None,None,None,pkresi=0,pkbond=0)

# Array of residues
seq = sequence.split(",")

# Get residue numbering .. potential bug here if number is inconsistent.. (Only works at c-terminal)
resi = int(cmd.get_model(sel).atom[0].resi) + 1
# Loop and build new residues
for i in range(1,repeat+1):
for s in seq:
# print "residue[%i]: %s %s" % (i,s,terminal)
editor.attach_amino_acid('pk1',s)

# Remove extra OXT carboxylate atom (OXT1, OXT2 ?) .. fix as needed
if terminal == 'C':
cmd.remove("%s and name OXT" % sel)

def set_phipsi(sel,phi,psi):
# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")

# Loop through atoms in selection
for at in atoms.atom:
if at.name == "N":
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "

try:
# Define residue selections
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
residue_def = unit_select+'resi '+str(at.resi)
# print "residue_def_prev: [%s]" % residue_def_prev
# print "residue_def : [%s]" % residue_def
if at.resn == "PRO":
print "Skipping setting phi for PRO"
else:
old_phi = cmd.get_dihedral(residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C')
cmd.set_dihedral( residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C' ,phi)
print "Changed residue %4s %4s phi: from %6.1f to %6.1f" % (at.resn, at.resi, old_phi, float(phi))
except:

print "Note skipping set of phi because of error; this is normal for a N-terminal residue"
try:
residue_def = unit_select+'resi '+str(at.resi)
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
# print "residue_def : [%s]" % residue_def
# print "residue_def_next: [%s]" % residue_def_next
old_psi = cmd.get_dihedral(residue_def +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N')
cmd.set_dihedral( residue_def +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N',psi)
print "Changed residue %4s %4s psi: from %6.1f to %6.1f" % (at.resn, at.resi, old_psi, float(psi))
except:
print "Note skipping set of psi; this is normal for a C terminal residue"

def getTableFromCsvFile(urlLocation):
result = []
r1 = urllib.urlopen(urlLocation)
data = r1.read()
r1.close()
dataLines = data.split("\n")
for dataLine in dataLines:
if dataLine:
result.append( dataLine.split(',') )
return result

# next line is a pymol directive.
python end

os.chdir("C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils")
seqInfo = getTableFromCsvFile("seqInfo.csv")
createPeptide(seqInfo)

</source>

[[Category:Script_Library|CreateSecondaryStructure]]
[[Category:Structural_Biology_Scripts|CreateSecondaryStructure]]

Jurgenfd at 14:01, 22 August 2007

2007-08-22T14:01:27Z

Jurgenfd: Added example

2007-08-21T01:16:41Z

Added example

Jurgenfd: Pretty big rewrite

2007-08-20T21:55:23Z

Pretty big rewrite

Show changes

Jurgenfd: /* SCRIPTS (CreateSecondaryStructures.py) */

2007-08-16T17:12:51Z

SCRIPTS (CreateSecondaryStructures.py)

Tmwsiy at 12:31, 12 October 2005

2005-10-12T12:31:32Z

Tmwsiy at 02:23, 9 September 2005

2005-09-09T02:23:23Z

Tmwsiy at 02:22, 9 September 2005

2005-09-09T02:22:06Z

New page

===DESCRIPTION===
To enable growing of a peptide sequence of one of the terminals. The growing can be set to any secondary structure (phi,psi pairing). Only extendHelix is currently implemented, but it should be rather simple to add more functions in or tweak the existing ones.

Functions:
*extendHelix
*createSS
*set_phipsi

===IMAGES===

===SETUP===
run CreateSecondaryStructure.py

===NOTES / STATUS===
*Tested on Pymolv0.97, Windows platform
*N-terminal growing doesn't work: adds residues, but doesn't set angles correctly

===USAGE===
extendHelix selection,sequence,repeat [, phi] [, psi] [, terminal ]
set_phipsi selection, phi, psi

===EXAMPLES===
extendHelix('resi 1371', 'ALA,GLN,HIS,ALA', 5)
set_phipsi('resi 1371', -60, -60)

===SCRIPTS (CreateSecondaryStructures.py)===
CreateSecondaryStructures.py
<source lang="python">

##############################################
# Author: Dan Kulp
# Date : 9/8/2005
#
#
# Notes:
# - Simple builds a string of residues
# and sets the phi,psi angles.
# - No energies are computed.
# - This will generate a starting point.
# - Defaultly grows from C-term,
# - N-term growing currently broken
#############################################

import string

# Wrapper Functions...
print "extendHelix(selection,sequence,repeat)"
print "Example:\n\t extendHelix('resi 1371', 'ALA,GLN,HIS,ALA', 5)"
print "Note: simple build of residue type and phi,psi angle; no energy computed"

def extendHelix(sel,seq,repeat=1,phi=-60,psi=-60,terminal='C'):
createSS(sel,seq,repeat,phi,psi,string.upper(terminal))
cmd.select("extendedHelix","all")
cmd.deselect()
cmd.save("./extendedHelix.pdb","extendedHelix")

# Create generic secondary structure, based off a selection
def createSS(sel, sequence='ALA',repeat='1',phi=-60,psi=-60,terminal='C'):

# Set selection
selection = "%s and name %s" % (sel,terminal)

# Pick atom for editing - interestingly only need to do this for the first addition
cmd.edit(selection,None,None,None,pkresi=0,pkbond=0)

# Array of residues
seq = string.split(sequence,",")

# Get residue numbering .. potential bug here if number is inconsistent.. (Only works at c-terminal)
resi = int(cmd.get_model(sel).atom[0].resi) + 1

# Loop and build new residues
for i in range(1,repeat+1):
for s in seq:
print "residue[%i]: %s" % (i,s)
editor.attach_amino_acid('pk1',s)

# Loop and set phi,psi angles for new residues
if terminal == 'N':
resi -= repeat

for i in range(0,repeat+1):
for s in seq:
set_phipsi("resi %i" % (resi), phi,psi)
resi += 1

# Remove extra OXT carboxylate atom (OXT1, OXT2 ?) .. fix as needed
if terminal == 'C':
cmd.remove("%s and name OXT" % sel)

def set_phipsi(sel,phi,psi):

# Set up some variables..
residues = ['dummy'] # Keep track of residues already done
probs = [] # probability of each residue conformation

# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")

# Loop through atoms in selection
for at in atoms.atom:
try:
# Don't process Glycines or Alanines
if at.resn == 'GLY' or at.chain+":"+at.resn+":"+at.resi in residues:
continue

residues.append(at.chain+":"+at.resn+":"+at.resi)

# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "

# Define selections for residue i-1, i and i+1
residue_def = unit_select+'resi '+str(at.resi)
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
# residue_def_next = unit_select+'resi '+str(int(at.resi)+1)

# Compute phi/psi angle
old_phi = cmd.get_dihedral(residue_def+' and name CB',residue_def+' and name CA',residue_def+' and name N',residue_def_prev+' and name C')
old_psi = cmd.get_dihedral(residue_def+' and name O',residue_def+' and name C',residue_def+' and name CA',residue_def+' and name CB')

print "Changing "+at.resn+str(at.resi)+" from "+str(old_phi)+","+str(old_psi)+" to "+str(phi)+","+str(psi)

cmd.set_dihedral(residue_def+' and name CB',residue_def+' and name CA',residue_def+' and name N',residue_def_prev+' and name C',phi)
cmd.set_dihedral(residue_def+' and name O',residue_def+' and name C',residue_def+' and name CA',residue_def+' and name CB', psi)

except:
print "Exception Thrown"
continue

</source>

[[Category:Script_Library|CreateSecondaryStructure]]

[[Category:Structural_Biology_Scripts|CreateSecondaryStructure]]

@@ Line 1: / Line 1: @@
 *Many bugs found, need to be worked out before further use... stay tuned.
@@ Line 59: / Line 58: @@
 # Create generic secondary structure, based off a selection
-def createSS(sel, sequence='ALA',repeat='1',phi=-60,psi=-60,terminal='C'):
+def createSS(sel, sequence='ALA',repeat=1,phi=-60,psi=-60,terminal='C'):
 	# Set selection

← Older revision	Revision as of 01:43, 28 March 2014
(No difference)

@@ Line 32: / Line 32: @@
+#
 #############################################
-# Call in pymol window like :
+# Call in window like :
 # @C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils\CreateSecondaryStructures.py
 # Next line is a pymol directive
@@ Line 58: / Line 58: @@
      for i in range( len(seqInfo) ):
          resi = 'resi '+`i+1`
-        print "Setting backbone angles for residue: ", i,   seqInfo[i][0],seqInfo[i][1],seqInfo[i][2]
+#        print "Setting backbone angles for residue: ", (i+1),   seqInfo[i][0],seqInfo[i][1],seqInfo[i][2]
          set_phipsi(resi,seqInfo[i][1],seqInfo[i][2])
@@ Line 108: / Line 108: @@
                  else:
                      old_phi = cmd.get_dihedral(residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C')
                      cmd.set_dihedral(          residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C'      ,phi)
              except:
                  print "Note skipping set of phi; this is normal for a N-terminal residue"
              try:
                  residue_def      = unit_select+'resi '+str(at.resi)
@@ Line 118: / Line 119: @@
 #                print "residue_def_next: [%s]" % residue_def_next
                  old_psi = cmd.get_dihedral(residue_def     +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N')
                  cmd.set_dihedral(          residue_def     +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N',psi)
              except:
                  print "Note skipping set of psi; this is normal for a C terminal residue"

@@ Line 11: / Line 11: @@
 ===USAGE===
 *seqInfo = getTableFromCsvFile("seqInfo.csv")
-  or
+  with in the file something like:
 *seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
 *createPeptide(seqInfo)

@@ Line 1: / Line 1: @@
 ===DESCRIPTION===
 To enable growing of a peptide sequence of one of the terminals.  The growing can be set to any secondary structure (phi,psi pairing). Only extendHelix is currently implemented, but it should be rather simple to add more functions in or tweak the existing ones.
@@ Line 13: / Line 16: @@
 *Tested on Pymolv0.97, Windows platform
 *N-terminal growing doesn't work: adds residues, but doesn't set angles correctly
 ===USAGE===

@@ Line 6: / Line 6: @@
 *createSS
 *set_phipsi
 ===SETUP===