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LoopBuilder builds in backbone atoms for loop regions where they are missing. However, these need to somehow be in the original PDB - this mover DOES NOT create the atoms and residues themselves! The backbones created by LoopBuilder will have ideal bond lengths, ideal bond angles, and torsions picked from a Ramachandran distribution. They should also not clash too badly with the surrounding protein. Other than that, these backbones are not optimized at all. But they are ready to be optimized by other movers. Under the hood, LoopBuilder uses KIC to build backbones.
Note that LoopModeler calls LoopBuilder, and that it's more common to use LoopModeler than it is to use LoopBuilder directly.
<LoopBuilder name="(&string)" max_attempts="(10000 &int)" loop_file="(&string)"> <Loop start="(&int)" stop="(&int)" cut="(&int)" skip_rate="(0.0 &real)" rebuild="(no &bool)"/> </LoopBuilder>
max_attempts: Building a backbone can take many attempts, because on each attempt KIC may fail to find a solution or may find a solution that clashes with the surrounding protein. That said, the default number of attempts is two or three orders of magnitude more than are usually needed, so I can't think of any situation in which you'd have to change this.