Re: [modeller_usage] loop refinement with disulfide patch

["M. Seigneuret" <>]

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()

--
Michel Seigneuret
Institut Cochin, U567-UMR8104
Département de Biologie Cellulaire
22 rue Méchain, 75014 Paris, France
Tel: 33 (0)1 40 51 64 50
Fax: 33 (0)1 40 51 64 54