Wed, 07/20/2016 - 13:36
#2
Helix-helix loop
I have a blue-blue-blue helix to helix loop, which is accepted by the ideal loop filter. In fact I made it by defining 3 segments as sheet and running ideal SS on the segments. But this color pattern is not in the list of ideal helix-helix loops shown in the Rama map.
Is this pattern missing in the list of of ideal loops or is it a mistake by the ideal loop filter?
Wed, 07/20/2016 - 18:28
#3
Missing from Rama Map
That particular helix-helix loop (and a couple others) is not shown in the Rama Map, but it is fairly common and should be accepted by the filter! Sorry for the inconsistency!
Wed, 07/20/2016 - 19:21
#4
Thanks for the quick answer.
Thanks for the quick answer.
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 85 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."