Hello,
I try to modeller my protein, and I had two different files which succerful good independely, but I need to uses the restrained from the firts file in combination of the symetry restrained of the second file.
Down, I just copied the type file I have used. How can I run both at the same time?
thank you !!
# Addition of restraints to the default ones from modeller import * from modeller.automodel import * # Load the automodel class
log.verbose() env = environ()
# directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']
class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: # rsr.append(file='my_rsrs1.rsr')
# Residues 20 through 30 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('20:', '30:'))) # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range('1:', '6:'))) rsr.add(secondary_structure.strand(self.residue_range('9:', '14:'))) # An anti-parallel sheet composed of the two strands: rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'], sheet_h_bonds=-5)) # Use the following instead for a *parallel* sheet: # rsr.add(secondary_structure.sheet(at['N:1'], at['O:9'], # sheet_h_bonds=5))
# Restrain the specified CA-CA distance to 10 angstroms (st. dev.=0.1) # Use a harmonic potential and X-Y distance group. rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CA:35'], at['CA:40']), mean=10.0, stdev=0.1))
a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', # codes of the templates sequence = '1fdx') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling
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# Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class
log.verbose()
# Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0)
env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']
# Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'twochain.ali' , # alignment filename knowns = '2abx', # codes of the templates sequence = '1hc9') # code of the target
a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling
*Example: examples/automodel/twochain.alihttp://salilab.org/modeller/examples/automodel/twochain.ali *
C; example for building multi-chain protein models
>P1;2abx structureX:2abx: 1 :A:74 :B:bungarotoxin:bungarus multicinctus:2.5:-1.00 IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG/ IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG*
>P1;1hc9 sequence:1hc9: 1 :A:148:B:undefined:undefined:-1.00:-1.00 IVCHTTATSPISAVTCPPGENLCYRKMWCDVFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG/ IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG*