I am trying to explore a range of different possible angles between two
domains of my protein by adding the following restraint (and modifying
the angle setting each time):
class mymodel(automodel):
def special_restraints(self, aln):
rsr = self.restraints
However, the results I've been getting are varying by far more than the
standard deviation I've set. The restraint is in the .rsr output file,
and the log files have not generated any insightful warnings or errors.
What modification should I make to more strictly enforce this restraint?
Also, can I get modeller to fail by setting the restraint to an extreme?
It would be useful to see your whole script - in particular, if you go
on to create an automodel object (rather than mymodel) then your
restraint won't be enforced at all.
The only way to "more strictly enforce" a restraint is to reduce its
standard deviation. Any violated restraints will be reported in the log
file.
To avoid confusion, I recommend that you don't use the old
restraint_parameters way of specifying restraints, but instead add them
in the new form introduced in Modeller 9 (see
http://salilab.org/modeller/manual/node194.html), i.e.