Quote:
"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." "
End quote.
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?
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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."