On 03/22/2011 11:33 AM, Giampaolo wrote: > I'm studying an homotetramer and i want to identify new sidechain > orientations on a specific helix segment without any more changes in the > protein structure of my initial pdb. So i tried the loopmodel routine:
loopmodel wasn't really designed or benchmarked for sidechain optimization, but what you're doing looks pretty reasonable here.
> ?- Is it possible to preserve the symmetry of the sidechains over all > the subunits? or...to perform a total symmetry of the models by a > post-processing step of refinement?
If you want the sidechains to be identical, it may make more sense to optimize a single chain, then construct the other chains by symmetry operations. You can apply a symmetry restraint, but it will compete with the loopmodel statistical potential, of course, so Modeller may not be able to satisfy it as well as you might want.
Ben Webb, Modeller Caretaker