My first issue is about bad contacts. When i produce models and evaluate them with procheck I always get some bad contacts. I have checked the procheck output files and noticed that all bad contacts always have a distance of 2.5 or 2.6 angstroms. Is there any way to change the minimum distance between atoms (i.e. increasing the different atom radii), since it seems like modeller and procheck have different opinions about what a bad contact is?
My second issue is about dimeric symmetry. I produced a model of a dimer using the automodel class and got some nice models. Then i wanted to produce the dimers with symmetry restraints and got many angles in disallowed regions, many bad contacts and very low G-factors. This seems very strange since the only difference between my two runs was that i requested symmetry in my second run. Why do my symmetrical dimers become so bad? These are my two different scripts:
from modeller import *
from modeller.automodel import *
env = environ()
a = automodel(env, alnfile='model-template.ali',
knowns='template', sequence='model',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 100
a.library_schedule = autosched.slow
a.max_var_iterations = 300
a.md_level = refine.slow
a.make()
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from modeller import *
from modeller.automodel import *
log.verbose()
class MyModel(automodel):
def special_restraints(self, aln):
s1 = selection(self.chains['A'])
s2 = selection(self.chains['B'])
self.restraints.symmetry.append(symmetry(s1, s2, 1.0))
def user_after_single_model(self):
self.restraints.symmetry.report(1.0)
env = environ()
a = MyModel(env, alnfile='chron1-2OBT.ali',
knowns='2OBT', sequence='chron1',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 100
a.library_schedule = autosched.slow
a.max_var_iterations = 300
a.md_level = refine.slow
a.make()
Thank you
/Niklas
