To run the OrientationalRestraintAndStructureFitter utility you can use the following command (something similar for your set up):

> java utilities/OrientationalRestraintAndStructureFitter -masterdir EXPERIMENTS/experimentsToTestUtilities/1ghh -pdbfile EXPERIMENTS/experimentsToTestUtilities/1ghh/1GHHModel1And2.pdb -rdctypes N_HN CA_C CA_HA -printbackcomputedrdcsincsrosettaformat -printbackcomputedrdcsinxplorformat -ranges 20 30 -printbackboneinpof -printbackbonedihedrals

To learn more about the command the options type: 

> java utilities/OrientationalRestraintAndStructureFitter -help


To run the StructureAligner utility you can use the following command (something similar for your set up):

> java utilities/StructureAligner -pdbfile  EXPERIMENTS/experimentsToTestUtilities/1ghh/1GHHModel1.pdb -pdbfile  EXPERIMENTS/experimentsToTestUtilities/1ghh/1GHHModel2.pdb -atomtypes N CA C -ranges 2 12 72 80

To learn more about the command the options type:

> java utilities/StructureAligner -help

To run the RDCSimulator utility you can use the following command (something similar for your set up):

> java utilities/RDCSimulator -masterdir EXPERIMENTS/experimentsToTestUtilities/1oyc/ -pdbfile EXPERIMENTS/experimentsToTestUtilities/1oyc/1oyc_afh.pdb -Szz 8.8465e-04 -Sxx_yy -1.2187e-03 -Sxy -6.5320e-04 -Sxz 6.0936e-05 -Syz 3.4005e-04 -rdctypes N_HN CA_C

To learn more about the command the options type:
    
> java utilities/RDCSimulator -help

