Agnieszka Szarecka wrote: > Problem 1: > > Is is possible in Modeller to fully optimize the specified loop but also > to allow a little bit of "adjustment freedom" to the loop end residues > (here 199 and 206)? If so, how should I modify the script?
The residues you select as the loop are optimized, and the remainder of the protein is not moved at all, so there is no real way to "half select" terminal residues in the way you propose. But there are a few things you could try. For example, you could extend the loop selection to include residues 199 and 206, but add additional position restraints on some or all atoms in those two residues to prevent them from moving too much. Alternatively, you could select only some of the atoms (for example, just the sidechain and part of the backbone) from those two residues.
> Problem 2: > > Could anyone advise on the m.loop.md_level? How should I judge what's > best for my loop?
Generally speaking, the longer the refinement you can afford, the better. But for longer loops the limiting factor is almost certainly the conformational sampling, which is probably easier to control by building more models rather than longer refinement.
Ben Webb, Modeller Caretaker