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 leuven@yeah.net
> 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() > > > http://main.jsp?urlfrom=..%2fread%2fread.jsp%3foffset%3d6%26mid%3d6%253a1tbiBhYpm0l0tYdswwAAsC%26sid%3dDAohKGSHhDjxWtvCvuHHsNJqqMBzelaw%26fid%3d1%26fr%3dfolder1&sid=DAohKGSHhDjxWtvCvuHHsNJqqMBzelaw&to=modeller_usage@salilab.org > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >