So I'm using the Chimera interface to Modeller and i'm slightly modifying the script that comes with Chimera to specify the secondary structure of my target...The biggest problem I'm seeing is that helices strands and loops which dont have a template structure
to align to (since the similairty is 60% and the identity is 30%) are just floating in space, they are not in a "natural" position. How do I fix that first? Secondly maybe it even is accepting the secondary structure restraint, but it is severly beding the
helices, since it wants to aggresivly align to the template structure...with which parameters would I handle this so I could get a reasonable structure? I'm inputing below the script that I'm using.
Thanks for the help!
Mark
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
# This script is generated by the Modeller Dialog in Chimera,
# incorporating the settings from the user interface. User can revise
# this script and submit the modified one into the Advanced Option panel.
# Import the Modeller module
from modeller import *
from modeller.automodel import *
# ---------------------- namelist.dat --------------------------------
# A "namelist.dat" file contains the file names, which was output from
# the Modeller dialog in Chimera based on user's selection.
# The first line it the name of the target sequence, the remaining
# lines are name of the template structures
namelist = open( 'namelist.dat', 'r' ).read().split('\n')
tarSeq = namelist[0]
template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] )
# ---------------------- namelist.dat --------------------------------
# This instructs Modeller to display all log output.
log.verbose()
# create a new Modeller environment
env = environ()
# Directory of atom/PDB/structure files. It is a relative path, inside
# a temp folder generated by Chimera. User can modify it and add their
# absolute path containing the structure files.
env.io.atom_files_directory = ['.', './template_struc']
# create a subclass of automodel or loopmodel, MyModel.
# user can further modify the MyModel class, to override certain routine.
class MyModel(automodel):
#def customised_function(self): pass
#code overrides the special_restraints method
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
rsr.add(secondary_structure.strand(self.residue_range('1:', '26:')))
rsr.add(secondary_structure.alpha(self.residue_range('27:', '50:')))
rsr.add(secondary_structure.strand(self.residue_range('51:', '62:')))
rsr.add(secondary_structure.alpha(self.residue_range('63:', '88:')))
rsr.add(secondary_structure.strand(self.residue_range('89:', '100:')))
rsr.add(secondary_structure.alpha(self.residue_range('101:', '127:')))
rsr.add(secondary_structure.strand(self.residue_range('128:', '136:')))
rsr.add(secondary_structure.alpha(self.residue_range('137:', '162:')))
rsr.add(secondary_structure.strand(self.residue_range('163:', '174:')))
rsr.add(secondary_structure.alpha(self.residue_range('175:', '201:')))
rsr.add(secondary_structure.strand(self.residue_range('202:', '204:')))
rsr.add(secondary_structure.alpha(self.residue_range('205:', '226:')))
rsr.add(secondary_structure.strand(self.residue_range('227:', '276:')))
rsr.add(secondary_structure.alpha(self.residue_range('277:', '303:')))
rsr.add(secondary_structure.strand(self.residue_range('304:', '312:')))
rsr.add(secondary_structure.alpha(self.residue_range('313:', '340:')))
rsr.add(secondary_structure.strand(self.residue_range('341:', '376:')))
rsr.add(secondary_structure.alpha(self.residue_range('377:', '400:')))
rsr.add(secondary_structure.strand(self.residue_range('401:', '420:')))
rsr.add(secondary_structure.alpha(self.residue_range('421:', '450:')))
rsr.add(secondary_structure.strand(self.residue_range('451:', '457:')))
rsr.add(secondary_structure.alpha(self.residue_range('458:', '483:')))
rsr.add(secondary_structure.strand(self.residue_range('484:', '485:')))
rsr.add(secondary_structure.alpha(self.residue_range('486:', '510:')))
rsr.add(secondary_structure.strand(self.residue_range('511:', '525:')))
rsr.add(secondary_structure.alpha(self.residue_range('526:', '551:')))
rsr.add(secondary_structure.strand(self.residue_range('552:', '638:')))
rsr.add(secondary_structure.alpha(self.residue_range('639:', '664:')))
#code overrides the special_patches method.
# e.g. to include the addtional disulfides.
#def special_patches(self, aln):
a = MyModel(env, sequence = tarSeq,
# alignment file with template codes and target sequence
alnfile = 'alignment.ali',
# PDB codes of the templates
knowns = template)
# index of the first model
a.starting_model = 1
# index of the last model
a.ending_model = 5
loopRefinement = False
# Assesses the quality of models using
# the DOPE (Discrete Optimized Protein Energy) method (Shen & Sali 2006)
# and the GA341 method (Melo et al 2002, John & Sali 2003)
a.assess_methods = (assess.GA341, assess.normalized_dope)
# ------------------------- build all models --------------------------
a.make()
# ---------- Accesing output data after modeling is complete ----------
# Get a list of all successfully built models from a.outputs
if loopRefinement:
ok_models = filter(lambda x: x['failure'] is None, a.loop.outputs)
else:
ok_models = filter(lambda x: x['failure'] is None, a.outputs)
# Rank the models by index number
#key = 'num'
#ok_models.sort(lambda a,b: cmp(a[key], b[key]))
def numSort(a, b, key="num"):
return cmp(a[key], b[key])
ok_models.sort(numSort)
# Output the list of ok_models to file ok_models.dat
fMoutput = open('ok_models.dat', 'w')
fMoutput.write('File name of aligned model\t GA341\t zDOPE \n')
for m in ok_models:
results = '%s\t' % m['name']
results += '%.5f\t' % m['GA341 score'][0]
results += '%.5f\n' % m['Normalized DOPE score']
fMoutput.write( results )
fMoutput.close()
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
# This script is generated by the Modeller Dialog in Chimera,
# incorporating the settings from the user interface. User can revise
# this script and submit the modified one into the Advanced Option panel.
# Import the Modeller module
from modeller import *
from modeller.automodel import *
# ---------------------- namelist.dat --------------------------------
# A "namelist.dat" file contains the file names, which was output from
# the Modeller dialog in Chimera based on user's selection.
# The first line it the name of the target sequence, the remaining
# lines are name of the template structures
namelist = open( 'namelist.dat', 'r' ).read().split('\n')
tarSeq = namelist[0]
template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] )
# ---------------------- namelist.dat --------------------------------
# This instructs Modeller to display all log output.
log.verbose()
# create a new Modeller environment
env = environ()
# Directory of atom/PDB/structure files. It is a relative path, inside
# a temp folder generated by Chimera. User can modify it and add their
# absolute path containing the structure files.
env.io.atom_files_directory = ['.', './template_struc']
# create a subclass of automodel or loopmodel, MyModel.
# user can further modify the MyModel class, to override certain routine.
class MyModel(automodel):
#def customised_function(self): pass
#code overrides the special_restraints method
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
rsr.add(secondary_structure.strand(self.residue_range('1:', '26:')))
rsr.add(secondary_structure.alpha(self.residue_range('27:', '50:')))
rsr.add(secondary_structure.strand(self.residue_range('51:', '62:')))
rsr.add(secondary_structure.alpha(self.residue_range('63:', '88:')))
rsr.add(secondary_structure.strand(self.residue_range('89:', '100:')))
rsr.add(secondary_structure.alpha(self.residue_range('101:', '127:')))
rsr.add(secondary_structure.strand(self.residue_range('128:', '136:')))
rsr.add(secondary_structure.alpha(self.residue_range('137:', '162:')))
rsr.add(secondary_structure.strand(self.residue_range('163:', '174:')))
rsr.add(secondary_structure.alpha(self.residue_range('175:', '201:')))
rsr.add(secondary_structure.strand(self.residue_range('202:', '204:')))
rsr.add(secondary_structure.alpha(self.residue_range('205:', '226:')))
rsr.add(secondary_structure.strand(self.residue_range('227:', '276:')))
rsr.add(secondary_structure.alpha(self.residue_range('277:', '303:')))
rsr.add(secondary_structure.strand(self.residue_range('304:', '312:')))
rsr.add(secondary_structure.alpha(self.residue_range('313:', '340:')))
rsr.add(secondary_structure.strand(self.residue_range('341:', '376:')))
rsr.add(secondary_structure.alpha(self.residue_range('377:', '400:')))
rsr.add(secondary_structure.strand(self.residue_range('401:', '420:')))
rsr.add(secondary_structure.alpha(self.residue_range('421:', '450:')))
rsr.add(secondary_structure.strand(self.residue_range('451:', '457:')))
rsr.add(secondary_structure.alpha(self.residue_range('458:', '483:')))
rsr.add(secondary_structure.strand(self.residue_range('484:', '485:')))
rsr.add(secondary_structure.alpha(self.residue_range('486:', '510:')))
rsr.add(secondary_structure.strand(self.residue_range('511:', '525:')))
rsr.add(secondary_structure.alpha(self.residue_range('526:', '551:')))
rsr.add(secondary_structure.strand(self.residue_range('552:', '638:')))
rsr.add(secondary_structure.alpha(self.residue_range('639:', '664:')))
#code overrides the special_patches method.
# e.g. to include the addtional disulfides.
#def special_patches(self, aln):
a = MyModel(env, sequence = tarSeq,
# alignment file with template codes and target sequence
alnfile = 'alignment.ali',
# PDB codes of the templates
knowns = template)
# index of the first model
a.starting_model = 1
# index of the last model
a.ending_model = 5
loopRefinement = False
# Assesses the quality of models using
# the DOPE (Discrete Optimized Protein Energy) method (Shen & Sali 2006)
# and the GA341 method (Melo et al 2002, John & Sali 2003)
a.assess_methods = (assess.GA341, assess.normalized_dope)
# ------------------------- build all models --------------------------
a.make()
# ---------- Accesing output data after modeling is complete ----------
# Get a list of all successfully built models from a.outputs
if loopRefinement:
ok_models = filter(lambda x: x['failure'] is None, a.loop.outputs)
else:
ok_models = filter(lambda x: x['failure'] is None, a.outputs)
# Rank the models by index number
#key = 'num'
#ok_models.sort(lambda a,b: cmp(a[key], b[key]))
def numSort(a, b, key="num"):
return cmp(a[key], b[key])
ok_models.sort(numSort)
# Output the list of ok_models to file ok_models.dat
fMoutput = open('ok_models.dat', 'w')
fMoutput.write('File name of aligned model\t GA341\t zDOPE \n')
for m in ok_models:
results = '%s\t' % m['name']
results += '%.5f\t' % m['GA341 score'][0]
results += '%.5f\n' % m['Normalized DOPE score']
fMoutput.write( results )
fMoutput.close()