Thanks. Unfortunately, the script stopped after a few seconds. Nothing special in the log (except that it was short), but this at the command prompt:
'import site' failed; use -v for traceback Traceback (most recent call last): File "model-loop.py, line 21, in ? m.make() File "C:\Program Files\Modeller9v3\modlib\modeller\automodel\loopmodel.py", line 31, in make self.build_seq(self.inimodel, 1) File "C:\Program Files\Modeller9v3\modlib\modeller\automodel\loopmodel.py", line 118, in build_seq self.create_loop_topology File "C:\Program Files\Modeller9v3\modlib\modeller\automodel\loopmodel.py", line 104, in create_loop_topology self.special_patches(aln) TypeError: special_patches() takes exactly 1 argument (2 given)
Strange. It seems to complain that special_patches has 2 arguments instead of 1, while it has actually 1 in your script and 2 in the manual examples. Thanks again for your help. Michel
Modeller Caretaker a écrit :
> It should be straightforward to modify this example to also override the > special_patches routine. In your case, your TOP script would translate > to something like: > > from modeller import * > from modeller.automodel import * > > env = environ() > > class MyLoop(loopmodel): > def select_loop_atoms(self): > return selection(self.residue_range('59:', '61:')) > def special_patches(self): > self.patch(residue_type='DISU', > residues=(self.residues['41'], > self.residues['60'])) > > m = MyLoop(env, > inimodel='mod2f.B99990002.pdb', > sequence='mod2134') > m.loop.starting_model = 20 > m.loop.ending_model = 30 > m.loop.md_level = refine.very_fast > m.make() >