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.
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.
Residue Count: Penalizes extra residues inserted beyond the 90 residue limit. Players may insert up to 10 extra residues.
Ideal Loops: Penalizes loops that do not conform to preferred ABEGO patterns. Use Auto Structures to see which residues count as "loops."
"The filter is meant to scan only loops, and will ignore any detected helices and sheets; use the Auto Structures tool to see which regions are considered "loops." "
Comment: The filter often show a bad loop segment that the Auto Structures tool has designated as part of a sheet or helix.
Is this normal?
Are all of the highlighted segments part of a sheet or helix? This shouldn't happen, and it would be helpful if you can share this solution with us.
Sometimes, at the edge of a bad loop, the Ideal Loop filter will also highlight one residue of the neighboring helix or sheet. This is just a quirk in the way we're highlighting residues, but it should not affect the filter penalty. The penalty from the Ideal Loop filter does not depend on loop length, e.g. a bad 6-residue loop receives the same penalty as a bad 5-residue loop.
yes - but is it intended?