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