Is it still possible to add symmetry restraints to automodel in spectial_restraints? I used to be able to do this with pick_atoms, but now that "selection" has taken over I seem to be missing something.
I define a new class as follows:
segsize=???
class sym_model(automodel): def special_restraints(self, aln): sel1 = selection(self.residue_range ('1',str(segsize))).only_mainchain() sel2 = selection(self.residue_range (str(segsize+1),str(2*segsize+1))).only_mainchain() self.restraints.symmetry.append(symmetry(sel1,sel2,1.0))
But get the following output:
File "model-dimer.py", line 41, in ? a.make() File "/usr/local/modeller9v2/modlib/modeller/automodel/automodel.py", line 99, in make self.homcsr(exit_stage) File "/usr/local/modeller9v2/modlib/modeller/automodel/automodel.py", line 423, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/local/modeller9v2/modlib/modeller/automodel/automodel.py", line 506, in mkhomcsr self.special_restraints(aln) File "model-dimer.py", line 26, in special_restraints sel1 = selection(self.residue_range('1',str(segsize))).only_mainchain() File "/usr/local/modeller9v2/modlib/modeller/coordinates.py", line 71, in residue_range start = self.residues[start]._num File "/usr/local/modeller9v2/modlib/modeller/coordinates.py", line 183, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/local/modeller9v2/modlib/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/local/modeller9v2/modlib/modeller/coordinates.py", line 56, in _indxres raise KeyError, ("No such residue: %s" % indx)
Thanks in advance