Loop definitions are used to identify the residues in a loop for loop modeling.
column1 "LOOP": Literally the string LOOP, identifying this line as a loop In the future loop specification files may take other data. column2 "integer": Loop start residue number column3 "integer": Loop end residue number column4 "integer": Cut point residue number, >=startRes, <=endRes. Default or 0: let LoopRebuild choose cutpoint randomly. column5 "float": Skip rate. default - never skip column6 "boolean": Extend loop. Default false
Residue numbers in loop definition files use Rosetta numbering, not PDB numbering.
For Example: A legal line in a loops file (the line by itself is a legal file):
Loop from residues 23-30 with the cutpoint at 26.
LOOP 23 30 26
-loop_file flag (and others) are just taking a file name or file path, so any name is fine as long as you specify it. For example:
my_protein.loops loopsfile loop_file top7.loops loops.txt