Treating of missing residues
Closed this issue · 2 comments
Currently (as far as I know):
- missing residues are ignored
- "loop" is left open, Rosetta does not "fuse" the ends (?)
--> add this info to the documentation
Wish-list:
- automatic modeling of missing residues up to a length of e.g. 3-5AA
- semi-automatic for lager loops (up to 15/20 AA), maybe even include available density information
Missing residues being ignored is standard in Rosetta. Fusing loops would lead to a huge strain on the bond length (indeed that's why we use the -missing_density_to_jump flag), so again not doing that is standard. It would be good to mention this in our standard Rosetta overview in the wiki. Of course it doesn't hurt to repeat it here but it's expected rather than specific to this pipeline.
Let's perhaps discuss separately how many missing residues we can add automatically, what we would gain and at what cost (as in, how much would we trust the results). Loops from 15res on are a challenging problem in itself, require substantial CPU time to model. Don't think we can include that for now. If density is available it's easier but that also requires a lot more knowledge by the user.
Added to the documentation and closed as not the scope of this pipeline