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
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