[modeller_usage] h-bonds with loop models

[David Gell <dagell AT mail.usyd.edu.au>]

Dear modellers

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?

any advice greatly received.

cheers
dave gell