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Re: [modeller_usage] disulfide building problem

If that is the code you used, I'd say try defining the class BEFORE you use it.

Put the "class automodel" part right after the "from modellier import *" part.


João [...] Rodrigues
@ http://stanford.edu/~joaor/

2009/12/6 leuven <">>
Dear All,
 I want to build a model including 3 disulfide bridges, but my script could not build bridges while modelling. Can you give me some suggestion on how to make the bridges-making script work?

from modeller import *
from modeller.automodel import *

env = environ()

env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7)
env.io.atom_files_directory = ['.', '../atom_files']

a = automodel(env, alnfile='GBSS1-mult.ali',knowns=('2r4tA','3copA','3cx4A'), sequence='GBSS1')

class automodel:
    def special_patches(self, aln):
        self.patch(residue_type='DISU', residues=(self.residues['151'],self.residues['181']))
        self.patch(residue_type='DISU', residues=(self.residues['422'],self.residues['448']))
        self.patch(residue_type='DISU', residues=(self! .residues['420'],self.residues['482']))

a.starting_model =1
a.ending_model = 60

a.library_schedule = autosched.slow
a.max_var_iterations = 300

a.md_level = refine.very_slow

a.repeat_optimization = 8
a.max_molpdf = 1e8


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