Re: [modeller_usage] Is the function - forms.upper_bound(..) - supposed to restrain precisely?

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

On 07/11/2012 12:42 PM, Adhikari, Badri (MU-Student) wrote:
> 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.

Modeller tries to satisfy all of the restraints as well as possible. 
This might not be achievable, of course (e.g. conflicting restraints).

If you want the restraint to be stronger, reduce the standard deviation.

> I also tried forms.upper_bound(group, feature, mean, stdev)

An upper bound is not the same as a Gaussian, so in general it doesn't 
make sense to switch one for another. For example, the two atoms could 
be zero angstroms apart and would not be penalized by the upper bound 
(but would be by a Gaussian).

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage