I'm making a new thread because it's off the topic, but I have a question in response to
this point:
> [Doggy structure improved, as shown by how] The Ramachandran plot tightened
This is interesting to me - other than eyeballing the plot, are there any quantitative metrics of Ramachandran distribution quality? At low-res or when refining a bunch of structures side-by-side it could be an additional indicator of quality of the model, without requiring having to inspect the plot. Of course manual inspection is always important in the end, but in early stages a global measure of spread could help guide refinement.
I've seen %outliers used for this purpose, but that ignores that while a residue can be "allowed" it can still be far from a statistically likely conformation. From what I've seen, some users only consult Ramachandran to tweak residues until they pop into the "allowed" regions and stop there, which isn't the same as globally improving the geometry.
Interested to hear thoughts (or it it's already in use, pointing me in the right direction!),
Shane Caldwell
McGill University