Dear modellers,
is it possible with Modeller4 to define constraints instead of restraints? I would like to constraint a set of conserved residues to be exactly in the same position as those of the template structure, and was looking for a way to do this without setting explicit distance, angle and torsion restraints.
Thank yuo very much,
Giulio Rastelli Dipartimento di Scienze farmaceutiche Universita di Modena , Italy
When you define a restraint, you choose the type of the restraint (like distance, angle etc) and the functional form how to restrain it. E.g. If the functional form defines only an upper boundary, you have a constraint.
For the various implemented functional forms check table 2.2. on p 74 in the manual.
a gaussian or an upper boundary gaussian (functional form 3 and 2) would be the answer for you. If you define a very small sigma for the G. function, you can imitate a hard limit, if it is desired. For options check MAKE_RESTRAINTS routine (therein: restraint_parameters).
Andras
Giulio Rastelli wrote: > > Dear modellers, > > is it possible with Modeller4 to define constraints instead of restraints? > I would like to constraint a set of conserved residues to be exactly in the > same position as those of the template structure, and was looking for a way > to do > this without setting explicit distance, angle and torsion restraints. > > Thank yuo very much, > > Giulio Rastelli > Dipartimento di Scienze farmaceutiche > Universita di Modena , Italy
there are two additional answers:
1) if you do not want to change some atoms relative to the initial conformation, they should not be selected for optimization. by default, all the atoms are selected for optimization. however, you can change that by redefining the select_atoms routine. you may want to think what kind of restraints are needed (selected-selected, selected-unselected atoms). please see faq.
2) there are no constraints in modeller. all are restraints.
best, andrej
Andras Fiser wrote:
> When you define a restraint, you choose the type of the restraint (like > distance, angle etc) and the functional form how to restrain it. E.g. If the > functional form defines only an upper boundary, you have a constraint. > > For the various implemented functional forms check table 2.2. on p 74 in the > manual. > > a gaussian or an upper boundary gaussian (functional form 3 and 2) would be the > answer for you. If you define a very small sigma for the G. function, you can > imitate a hard limit, if it is desired. For options check MAKE_RESTRAINTS > routine (therein: restraint_parameters). > > Andras > > Giulio Rastelli wrote: > > > > Dear modellers, > > > > is it possible with Modeller4 to define constraints instead of restraints? > > I would like to constraint a set of conserved residues to be exactly in the > > same position as those of the template structure, and was looking for a way > > to do > > this without setting explicit distance, angle and torsion restraints. > > > > Thank yuo very much, > > > > Giulio Rastelli > > Dipartimento di Scienze farmaceutiche > > Universita di Modena , Italy > > -- > , > Andras Fiser, PhD # phone: (212) 327 7216 > The Rockefeller University # fax: (212) 327 7540 > Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu > New York, NY 10021-6399, USA # http://salilab.org/~andras
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Andras Fiser -
Andrej Sali -
Giulio Rastelli