Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.
Core Existence: Ensures that at least 30% of the residues are buried in the core of your design.
Fragment Score: Scans for parts of your design that are unlikely to fold up naturally. Use Rebuild and Remix tools to fix these regions of your design!
Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.
Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets. Also penalizes hydrophilic residues in the core and hydrophobic residues on the surface.
any chance of modifying the mutate function, rather than having to go back and do it by hand each time one uses it.
You mean, modify the mutate function so it adheres to filter rules?
Sometimes the Mutate function does make a mutation that causes a filter to fail; I agree this behavior is undesired and also inefficient. This fix is high on the to-do list, and hopefully will be added soon.
gly in the loops between sheets is getting penalised.
Could you share this solution with us, so I can take a closer look?