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Re: [modeller_usage] Specify Angle Restraint

Brandon Mills wrote:
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
rsr.add(atom_ids=('O:67', 'CE3:146', 'CA:149'), restraint_parameters=(3, 1, 2, 2, 3, 2, 1, 2.618, 0.010)) 
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.

    rsr = self.restraints
    a = self.atoms
    f = forms.gaussian(group=physical.angle,
                       feature=features.angle(a['O:67'],
                                              a['CE3:146'],
                                              a['CA:149']),
                       mean=2.618, stdev=0.010)
    rsr.add(f)

	Ben Webb, Modeller Caretaker
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