Hello,
we are trying to build a symmetric hexamer of a 735 aa protein molecule. Modelling the monomer works without problems. For the hexamer, we have generated the hexameric template and replicated the target sequence in the alignment file accordingly. This works flawlessly, as well. However, if we insert these symmetry retraints (adopted from the example in the manual)
------------------------------------------- # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') s5 = selection(self.chains['E']).only_atom_types('CA') s6 = selection(self.chains['F']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, s5, s6, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) -------------------------------------------
leaving both alignment and template files untouched, then the program stops with the following error:
------------------------------------------- Traceback (most recent call last): File "get-model2.py", line 42, in ? a.make() # do homology modeling File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 436, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 524, in mkhomcsr self.special_restraints(aln) File "get-model2.py", line 23, in special_restraints self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, s5, s6, 1.0)) TypeError: __init__() takes exactly 4 arguments (8 given) -------------------------------------------
We are a bit lost here :( Which init call is the message referring to? Any ideas how to resolve this?
Oliver
------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich
Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------