Hi list,

Im trying to model a 5 chains protein, wich 3 of them are long alpha-helix. Well, I would like to set some residues as part of these helixes, and a SS bridge. When I try to tell modeller 9v1 to do that (with the enclose script), I keep receiving the following error: ---------------------------------------------------------------------------- C:\teste2>mod9v1 model_ss_alpha.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "model_ss_alpha.py", line 31, in ? a.make() File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel .py", line 108, in make self.homcsr(exit_stage) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel .py", line 419, in homcsr self.make_initial_model(aln) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel .py", line 433, in make_initial_model self.generate_method(self, aln) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\generate. py", line 25, in transfer_xyz mdl.create_topology(aln) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel .py", line 605, in create_topology self.special_patches(aln) File "model_ss_alpha.py", line 18, in special_patches self.patch(residue_type='DISU', residues=(self.residues['1070'], File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\coordinates.py", li ne 165, in __getitem__ (self.offset, self.length, self.suffix)) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\util\modutil.py", l ine 76, in handle_seq_indx int_indx = lookup_func(*args) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\coordinates.py", li ne 50, in _indxres raise KeyError, ("No such residue: %s" % indx) KeyError: 'No such residue: 1070' -------------------------------------------------------------------------- What might be wrong?

Thanks,

Aline

------------------------------------------------------------------- This is the script:

from modeller import * # Load standard Modeller classes from modeller.automodel import *

# Redefine the special_restraints routine to include the secondary # structure restraints (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints # An alpha-helix: rsr.make(aln, restraint_type='ALPHA', residue_ids= ('1118:', '1131:'), spline_on_site=False) # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class mymodel(automodel): def special_patches(self, aln): # A disulfide between residues 8 and 45: self.patch(residue_type='DISU', residues=(self.residues['1070'], self.residues['1122']))

# This is as usual: log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' env.io.hetatm = env.io.water = True a = mymodel(env, alnfile='a6b1lam.ali', knowns=('a6b1lam_model_0.3'), sequence='a6b1_lam') a.starting_model = 1 a.ending_model = 1 a.make()