Dear All, I have a problem with restraints after loop refeinement, in particular the distances between some atoms do not respect the restraint values set up. These values are respected after model building (without a slow MD) but not after loop refinements. I didn't use any refinement of imput model.
I show the used scripts: This is for automodel: from modeller import * from modeller.automodel import * # Load the automodel class
log.verbose() env = environ()
env.io.atom_files_directory = ['.', '../atom_files']
class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms
rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NZ:114'], at['OD1:288']), mean=2.6, stdev=0.1))
rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NE:136'], at['OD1:260']), mean=2.6, stdev=0.3))
a = MyModel (env, alnfile='allinea.pir', knowns='AB, BC', sequence='CD') a.starting_model = 1 a.ending_model = 1
a.md_level = refine.very_fast
a.make()
This is for loop refinement:
log.verbose() env = environ()
a = loopmodel(env, alnfile = 'allinea.pir', # alignment filename knowns = ''AB, BC', # codes of the templates sequence = 'CD') # 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. md_level = None # No refinement of model
a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model
a.loop.md_level = refine.fast # Loop model refinement level
a.make()
Thank you very much in advance
Mario