Hello modeller users and experts,
I am trying to impose distance restrains in structure prediction python script as explained in the example at
http://salilab.org/modeller/manual/node27.html. Following the example I used the
forms.gaussian(group, feature, mean, stdev)
function. But my predicted model does exactly satisfy the distance restrain. I can observe that adding the distance restrain, HAS added some distance restrain but it looks like modeller is not giving 100% weightage to the distance restrain.
I also tried
forms.upper_bound(group, feature, mean, stdev) as
explained at
http://salilab.org/modeller/9v5/manual/node97.html. With this function, I verified that modeller gives more weightage to the distance restrain, but STILL does not precisely satisfy the restrain.
Is this what these functions are supposed to do? OR is there any other technique to instruct modeller to absolutely satisfy the distance restrain?
Case I:
Restrain used:
rsr.add(forms.gaussian(group = physical.xy_distance, feature = features.distance(at['CA:2'], at['CA:4']), mean = 7.0, stdev = 0.1));
Distance between
CA:2 and CA:4 in the final model: 8.5
Case II:
Restrain used: rsr.add(forms.upper_bound(group = physical.xy_distance, feature = features.distance(at['CA:2'], at['CA:4']), mean = 7.0, stdev = 0.1));
Distance between
CA:2 and CA:4
in the final model: 8.2
Sincerely,
Badri Adhikari
CS Graduate Student,
University of Missouri-Columbia,
Columbia, Missouri