From Jacobson Lab Wiki
loop is a top level plop command that will initiate loop prediction and related subcommands in Plop. Generally, the loop command is followed by one of the sub-commands listed below and the loop bounds in standard Plop residue format. For example:
loop predict A:10 A:15 [ options ]
predicts the loop from residue A:10 to A:15.
 loop find
 loop sample
 loop contact
"contact," as in energy
 loop predict
Begins a single loop prediction run. If the loop includes a helix that will be built, the
helix_build command and the first and last helix residues must be specified immediately following the
loop predict A:10 A:15 command. For example:
loop predict A:10 A:25 helix_build A:12 A:18
 loop validate
Similar to loop predict...
 loop mc
Loop Monte Carlo
 loop quality
 loop surroundings
List the residues surrounding a set of predicted loops. Expects the
sidecut option. For example:
loop surr A:10 A:15 sidecut 7.5
This command will perform an initial backbone buildup and list all residues within 7.5 angstroms from the initial set of loops. No clustering or side optimization is carried out after the buildup.
 loop score
Performs an energy calculate on the protein after loading loop residues and associated rotamer libraries, so that any pseudo-energy terms related to loop rotamers can be included in the energy calculation.
add_clust yes/no - alt_rms_intvl - alternative loop bounds to use for RMSD calculation only alt_scoring_intvl - alternative loop bounds to use for loop-based scoring only ana yes/no - analytical closure angcut - angcut_auto - backmin yes/no - buried - check_with_segment - checks phi, psi against the dipeptide library independent of library used to sample cling - clust - clust_atom - concut - constrain - cartesian constraint to within x angstrom of a fixed point eclust - exposed - failsafe yes/no - ideal yes/no - longloop - loopfile - maefile - maxangdev - constrain dihedral to within x degrees of starting maxcalpha - cartesian constraint to within x angstrom of starting maxhelixdev - constrain dihedral to within x degrees of ideal helix maxstranddev - constrain dihedral to within x degrees of ideal strand mc - set mc params membrane - mid_loop - mid_move - midrescons - min - set min params mpass - native_opt yes/no - minimize & side opt on native nclust - nclust_stage - nconf_init - nconf_min - niter - niter_side - nonstan back/side - noscoptfile - nres_stage - ofac - overlap factor; default = 0.65 omega - pdbfile - perturb_angle - perturb option in analytical closure perturb_level - perturb option in analytical closure rand - rmsdfile - rmsdtype - user-specified RMSDs in addition to defaults. Requires align and/or rmsd keyword, e.g., "rmsdtype align calpha A:1 A:5 rmsd A:2 A:4" or "rmsdtype rmsd ncaco A:2 A:4" (global alignment) segment yes/no - default to dipeptide library for loops > 13 residues, or LHL halves > 6 residues. side1 - side2 - sideadd - add a list of additional residues sidecut - sidefrz - sideres - statrmsd yes/no - summfile - tether - tree_verb -