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Difference between revisions of "CreateSecondaryStructure"

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===DESCRIPTION===
 
===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.
+
To build a peptide sequence.   
−
 
 
−
Functions:
 
−
*extendHelix
 
−
*createSS
 
−
*set_phipsi
 
  
 
===SETUP===
 
===SETUP===
Line 11: Line 6:
  
 
===NOTES / STATUS===
 
===NOTES / STATUS===
−
*Tested on Pymolv0.97, Windows platform
+
*Tested on Pymolv1.0, Windows platform
−
*N-terminal growing doesn't work: adds residues, but doesn't set angles correctly
+
*Many bugs to be found
  
 
===USAGE===
 
===USAGE===
−
  extendHelix selection,sequence,repeat [, phi] [, psi] [, terminal ]
+
*seqInfo = getTableFromCsvFile("seqInfo.csv")
−
set_phipsi selection, phi, psi
+
  with in the file something like:
 +
MET,-54,-47
 +
PRO,-54,-47
 +
 
 +
*seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
 +
*createPeptide(seqInfo)
  
 
===EXAMPLES===
 
===EXAMPLES===
−
  extendHelix('resi 1371', 'ALA,GLN,HIS,ALA', 5)
+
  seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
−
set_phipsi('resi 1371', -60, -60)
+
createPeptide(seqInfo)
  
 
===SCRIPTS (CreateSecondaryStructures.py)===
 
===SCRIPTS (CreateSecondaryStructures.py)===
 
CreateSecondaryStructures.py  
 
CreateSecondaryStructures.py  
 
  <source lang="python">
 
  <source lang="python">
−
 
 
##############################################
 
##############################################
−
#  Author:  Dan Kulp
+
#  Original Author:  Dan Kulp
 
#  Date  :  9/8/2005
 
#  Date  :  9/8/2005
 +
#    MOdified by Jurgen F. Doreleijers
 +
#    For Hamid Eghbalnia             
 
#
 
#
−
#
 
−
#  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
 
 
#############################################
 
#############################################
−
 
+
# Call in window like :
−
import string
+
# @C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils\CreateSecondaryStructures.py
−
 
+
# Next line is a pymol directive
−
# Wrapper Functions...
+
python
−
print "extendHelix(selection,sequence,repeat)"
+
import urllib
−
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")
 
  
  
 +
# 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
 
# 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,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
+
    # Set selection
−
cmd.edit(selection,None,None,None,pkresi=0,pkbond=0)
+
    selection = "%s and name %s" % (sel,terminal)
  
−
# Array of residues
+
    # Pick atom for editing - interestingly only need to do this for the first addition
−
seq = string.split(sequence,",")
+
    cmd.edit(selection,None,None,None,pkresi=0,pkbond=0)
  
−
# Get residue numbering .. potential bug here if number is inconsistent.. (Only works at c-terminal)
+
    # Array of residues
−
resi = int(cmd.get_model(sel).atom[0].resi) + 1
+
    seq = sequence.split(",")
−
 
−
# 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
+
    # Get residue numbering .. potential bug here if number is inconsistent.. (Only works at c-terminal)
−
if terminal == 'N':
+
    resi = int(cmd.get_model(sel).atom[0].resi) + 1
−
resi -= repeat
+
    # Loop and build new residues
−
+
    for i in range(1,repeat+1):
−
for i in range(0,repeat+1):
+
        for s in seq:
−
for s in seq:
+
#            print "residue[%i]: %s %s" % (i,s,terminal)
−
set_phipsi("resi %i" % (resi), phi,psi)
+
            editor.attach_amino_acid('pk1',s)
−
resi += 1
 
  
−
# Remove extra OXT carboxylate atom (OXT1, OXT2 ?) .. fix as needed
+
    # Remove extra OXT carboxylate atom (OXT1, OXT2 ?) .. fix as needed
−
if terminal == 'C':
+
    if terminal == 'C':
−
cmd.remove("%s and name OXT" % sel)
+
        cmd.remove("%s and name OXT" % sel)
−
+
   
−
+
   
 
def set_phipsi(sel,phi,psi):
 
def set_phipsi(sel,phi,psi):
 +
    # Get atoms from selection
 +
    atoms = cmd.get_model("byres ("+sel+")")
  
−
# Set up some variables..
+
    # Loop through atoms in selection      
−
residues = ['dummy']  # Keep track of residues already done
+
    for at in atoms.atom:
−
probs = []            # probability of each residue conformation
+
        if at.name == "N":
−
 
+
            # Check for a null chain id (some PDBs contain this)  
−
# Get atoms from selection
+
            unit_select = ""
−
atoms = cmd.get_model("byres ("+sel+")")
+
            if not at.chain == "":
−
 
+
              unit_select = "chain "+str(at.chain)+" and "
−
        # Loop through atoms in selection
+
   
−
for at in atoms.atom:
+
            try:
−
    try:
+
                # Define residue selections    
−
      # Don't process Glycines or Alanines
+
                residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
−
if at.resn == 'GLY' or at.chain+":"+at.resn+":"+at.resi in residues:
+
                residue_def      = unit_select+'resi '+str(at.resi)      
−
continue
+
#                print "residue_def_prev: [%s]" % residue_def_prev
−
 
+
#               print "residue_def    : [%s]" % residue_def
−
        residues.append(at.chain+":"+at.resn+":"+at.resi)
+
                if at.resn == "PRO":
−
 
+
                    print "Skipping setting phi for PRO"
−
        # Check for a null chain id (some PDBs contain this)  
+
                else:
−
        unit_select = ""
+
                    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')      
−
if not at.chain == "":
+
                    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)
−
  unit_select = "chain "+str(at.chain)+" and "
+
                    print "Changed residue %4s %4s phi: from %6.1f to %6.1f" % (at.resn, at.resi, old_phi, float(phi))      
−
 
+
            except:
−
        # Define selections for residue i-1, i and i+1   
+
               
−
residue_def = unit_select+'resi '+str(at.resi)
+
                print "Note skipping set of phi because of error; this is normal for a N-terminal residue"
−
  residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
+
            try:
−
# residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
+
                residue_def      = unit_select+'resi '+str(at.resi)
−
 
+
                residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
−
        # Compute phi/psi angle
+
#                print "residue_def    : [%s]" % residue_def
−
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')
+
#                print "residue_def_next: [%s]" % residue_def_next
−
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')
+
                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 "Changing "+at.resn+str(at.resi)+" from "+str(old_phi)+","+str(old_psi)+" to "+str(phi)+","+str(psi)
+
                print "Changed residue %4s %4s psi: from %6.1f to %6.1f" % (at.resn, at.resi, old_psi, float(psi))       
−
 
+
            except:
−
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)
+
                print "Note skipping set of psi; this is normal for a C terminal residue"
−
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
 
  
 +
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>
 
</source>
Line 137: Line 145:
  
 
[[Category:Script_Library|CreateSecondaryStructure]]
 
[[Category:Script_Library|CreateSecondaryStructure]]
−
 
 
[[Category:Structural_Biology_Scripts|CreateSecondaryStructure]]
 
[[Category:Structural_Biology_Scripts|CreateSecondaryStructure]]

Latest revision as of 01:43, 28 March 2014

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 

##############################################
#   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)
Retrieved from "http://wiki.pymol.org/index.php?title=CreateSecondaryStructure&oldid=5344"