[modeller_usage] Is there anything wrong with my configuration file?My models look so strange

["wayj86 wayj86" <>]

Hi all,

 

Two days ago I wanted to model an antibody with specifying the CDR regions.Here is my configuation file:

 

# Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

 

# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class mymodel(loopmodel):
    def special_patches(self, aln):
        # A disulfide between residues 22 and 96:
        self.patch(residue_type='DISU', residues=(self.residues['22'],
                                                  self.residues['95']))
        self.patch(residue_type='DISU', residues=(self.residues['158'],
                                                  self.residues['228']))
    def select_loop_atoms(self):
        return selection(self.residue_range('26','33'),self.residue_range('51','57'),self.residue_range('96','110'),self.residue_range('162','172'),self.residue_range('190','192'),self.residue_range('229','237'))

 

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

 

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

 

a = mymodel(env,
            alnfile  = '3.ali',     # alignment filename
            knowns   = ('HL','y','121','113'),              # codes of the templates
            sequence = '6b4',
     loop_assess_methods=assess.DOPE)              # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model  = 8                 # index of the last model
                                    # (determines how many models to calculate)
a.loop.starting_model=1
a.loop.ending_model=2

 

a.make()                            # do the actual homology modeling

 

 

I don't know what is wrong with it but the models it built were so strange,I can see some breakpoints in the structures.


However,if I delete the sentences for loops specifying,the breakpoints would disappear.

# Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class mymodel(loopmodel):
    def special_patches(self, aln):
        # A disulfide between residues 22 and 96:
        self.patch(residue_type='DISU', residues=(self.residues['22'],
                                                  self.residues['95']))
        self.patch(residue_type='DISU', residues=(self.residues['158'],
                                                  self.residues['228']))

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

a = mymodel(env,
            alnfile  = '3.ali',     # alignment filename
            knowns   = ('HL','y','121','113'),              # codes of the templates

            sequence = '6b4')

a.starting_model= 1                 # index of the first model
a.ending_model  = 8                 # index of the last model
                                    # (determines how many models to calculate)

a.make()                            # do the actual homology modeling

So could you please tell me how can I specify the CDR loops correctly?Thank you very much for any help.

 

Best wishes,

Stanley

 

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