qiuyan_wang@email.jlu.edu.cn wrote: > Dear my modellers: I am modeling a chimeric protein from two > different proteins, which have known structures. There is no overlap > between them,so i oriented two domains before the modeling. But i got > an unreasonable model in which one domain so called 'lid' was just > beside the other catalytic domain,even under some distance restraints > to some reference residues i used. It is believed that hydrophobic > interaction drives two domains forming a closed conformation. > So,should i use something like hydrophobic restraints to the > modeling, and how to do this?

Modeller has no explicit hydrophobic restraints, and no explicit solvent (any solvation information will be taken implicitly from your templates). If you do not have a template structure containing the domain-domain interaction, you will have to approximate it yourself using distance restraints.

Ben Webb, Modeller Caretaker