Re: [modeller_usage] Specify Angle Restraint

[Modeller Caretaker <modeller-care@ucsf.edu>]

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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