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()
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 > >
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 anaryin@gmail.com 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/ http://stanford.edu/%7Ejoaor/ > > > > 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 >> >> >
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