On 9/20/22 8:52 AM, Joel Subach via modeller_usage wrote: > Hi, I loop missing residue MODELLER modeled a heptamer both > unrestrained and restrained with the former exhibiting an RMSD > of 0.295 while the restrained exhibited an RMSD of 0.0. > > The restrained model´s missing residue loops, however, are too > dynamic and seem to be broken when visualized via Pymol. > Accordingly, is there a way to generate the restrained version to > exhibit intact loops so that I may keep this version because of its > 0.0 RMSD?
When you have regions like this that are not aligned with a template, the only restraints on them in standard comparative modeling are from the CHARMM forcefield. This will attempt to generate sensible stereochemistry, but if you want more native-looking loops, you'll want to refine them using the loop modeling protocol. You have long loops though - you'll definitely need to build at least several hundred loop models. If they still look too constrained, you might consider broadening the residue range in your selection to include a few residues either side of the loop.
Ben Webb, Modeller Caretaker