Application purpose

Loop definitions are used to identify the residues in a loop for loop modeling.

File Format

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.

Example

For Example: A legal line in a loops file (the line by itself is a legal file):

LOOP 23 30 26

Loop from residues 23-30 with the cutpoint at 26.

Name

Rosetta's -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

Loops File

Application purpose

File Format

Example

Name

See Also