Re: [modeller_usage] disulfide building problem

[João Rodrigues <>]

Oops, sorry, I just missed one thing.

The class you should define should be something like this:

class MyModel(automodel):
  def special_patches(self ......):
    ........

There is a very clear page about this in the manual:

http://salilab.org/modeller/manual/node24.html

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

On Sun, Dec 6, 2009 at 9:59 AM, João Rodrigues <">> wrote:

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.

Regards

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

2009/12/6 leuven <" target="_blank">>

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 *

log.verbose()
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

a.use_parallel_job(j)     
a.make()

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