Dear Modeller's users

I want to add a helix restraint to some residues in each monomer of my homodimer model, I followed the example given in Modeller 9v8 Manual but It gives me the following error (Is it a residue numbering problem?):

KeyError: 'No such residue: 29:'

This is my alignment file, which worked well without adding the helix restraint:

>P1; TCP15_dimer2 sequence:TCP15_dimer2:::::::0.00:0.00 -KDRHTKVEGRGRRIRMPAMCAARVFQLTRELGHKSDGE-----------TIEWLLQQAE P-AVIAA----- / -KDRHTKVEGRGRRIRMPAMCAARVFQLTRELGHKSDGE-----------TIEWLLQQAE P-AVIAA----- / .................. / .................. * >P1; 1nlw_D_E structureX:1nlw_D_E:503:D:819:J:::-1.00:-1.00 -RSTHNEMEKN-RRAHLRLSLE-KLKGL-----------VPLGPDSSRHTTL-SLLTKAK LHIKKLE----- / --AHHNALERK-RRDHIKDSFH-SLRDS-----------VPSLQ-GEKASRA-QILDKAT EYIQYMRR---- / .................. <--- DNA chain 1 / .................. <---DNA chain 2 *

This is the script I used:

from modeller import * from modeller.automodel import * # Load the automodel class

log.verbose()

env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True <---- This is added because my model also include a small DNA molecule

class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Residues restraints for the first monomer: rsr.add(secondary_structure.alpha(self.residue_range('29:', '32:'))) rsr.add(secondary_structure.alpha(self.residue_range('38:', '39:')))

# Residues restraints for the second monomer: rsr.add(secondary_structure.alpha(self.residue_range('111:', '114:'))) rsr.add(secondary_structure.alpha(self.residue_range('121:', '122:')))

a = MyModel(env, alnfile = 'alignment_2.ali' , # alignment filename knowns = '1nlw_D_E' , # codes of the templates sequence = 'TCP15_dimer2') # code of the target

a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling

Any suggestion will be appreciated