David Gell wrote: > i am trying to build models for a single missing loop on a known xtal > structure and i have a couple of questions > > 1) can modeller introduce hydrogen bonds in loop modelling (is > it true that all-hydrogen models are not fully implemented for loop > modelling)? > > 2) is it true that modeller does not include hydrophobic packing factors? > i currently have models with fully exposed hydrophobics that have similar > 'modeller objective function' to those with more buried hydrophobic > sidechains. > > i'm a modeller newbie, and above is based on my understanding (i.e. > likely flawed) of the mail archives and docs. perhaps i should be > introducing some 'artificial' distance restraints to mimic the effects of > the above interactions?
You are exactly correct on all points. The loop modeling potential acts only on heavy atoms - there are no explicit hydrogen bonds. There is also no explicit consideration of hydrophobic packing - this is implicit in distance restraints inherited from the template, and is thus missing for loop regions. You could, however, use the dope_loopmodel class rather than loopmodel, which includes GB/SA implicit solvation, to remedy this somewhat.
As you say, you can certainly add your own distance restraints if you are aware of any specific interactions.
Ben Webb, Modeller Caretaker