Programs of the NMRPipe System
DC: General-Purpose Dipolar Coupling Analysis and Protein Backbone Chemical Shift Prediction.

Arguments for Simulation (Zero Values for Auto):
Flag Argument Default Description
 -pdb pName None PDB Input (Required).
 -inD dName None Dipolar Coupling Input.
 -inCS csName None Chemical Shift Input.
 -outD dName None Simulated Coupling Output.
 -outCS csName None Simulated Shift Output.
 -sPath sPath SURF_DIR Path to Surface Files.
PDB Residue Selection Mode (0 for Auto):
 -a1 aRes1 0 First Res in PDB.
 -r1 res1 0 First Res in Table Segment (Also: -s1).
 -rN resN 0 Last Res in Table Segment (Also: -sN).
Dipolar Coupling Residue Selection Mode:
 -excl Both ResI and ResJ in Range res1 to resN.
 -inclAll Either ResI or ResJ in Range (Also: -incl).
 -inclMin Min(ResI,ResJ) in Range.
 -inclMax Max(ResI,ResJ) in Range (Default).
Dipolar Interaction Value Calculation:
 -fixedDI Use Fixed Values When Possible (Default).
 -nofixedDI Always Use Values from PDB Distances.
 -keepDI Keep Existing Values, if Any.
Other Arguments:
 -w wList List of Weights for Segment.
 -constRMS Use Fixed Estimate of CS RMS.
 -retry nR 0 Retry DC Fit with Multiple Start Points.
 -retry Retry DC Fit 8 Times (Old Usage).
 -noretry Single DC Fit Only (Old Usage).
 -ignore Ignore PDB Segment and Chain Info.
 -dc DC Table Source.
 -reset Reset Tensor Values to Defaults.
 -verb Verbose mode ON.
Alignment Tensor Specification Methods:
 -svd SVD Calc of Saupe Matrix (Default).
 -saupe sList List of 5 Saupe Values (also: -align).
 -fit Nonlinear Fit with Variation of one or
  more of: Da, Dr or Rh, and Rotations.
 -fixed Fixed Da, Dr or Rh, and Rotations.
 -nofixed Same as -fit.
Predefined Nonlinear Fitting Modes (Use Only One):
 -dadr Fixed Da and Dr, Variable Rotations.
 -rot Fixed Rotations, Variable Da and Dr.
 -rotdr Fixed Dr and Rotations, Variable Da.
 -rotrh Fixed Rh and Rotations, Variable Da.
Alignment Tensor Magnitude (Da) Limits:
 -da da 1.0e-4 Initial Da Value.
 -daMin daMin -1.0e-2 Minimum Da Value.
 -daMax daMax 1.0e-2 Maximum Da Value.
Alignment Tensor Dr or Rhombicity Limits:
 -dr dr 1.0e-5 Initial Dr Value.
 -drMin drMin -1.0e-2 Minimum Dr Value.
 -drMax drMax 1.0e-2 Maximum Dr Value.
 -rh rh 0.1 Initial Rhombicity Value.
 -rhMin rhMin 0.0 Minimum Rhombicity Value.
 -rhMax rhMax 0.6666 Maximum Rhombicity Value.
Rotation Starting Parameters (Also -rx -ry etc):
 -psi psi 45.0 Initial X-Axis Rotation.
 -psiMax psiMax 180.0 Maximum X-Axis Rotation.
 -psiMin psiMin -180.0 Minimum X-Axis Rotation.
 -theta theta 45.0 Initial Y-Axis Rotation.
 -thetaMax thetaMax 180.0 Maximum Y-Axis Rotation.
 -thetaMin thetaMin -180.0 Minimum Y-Axis Rotation.
 -phi phi 45.0 Initial Z-Axis Rotation.
 -phiMax phiMax 180.0 Maximum Z-Axis Rotation.
 -phiMin phiMin -180.0 Minimum Z-Axis Rotation.
 -auto Use SVD for Initial Angles.
Rotation Offsets (Also -rxOff -ryOff -rzOff):
 -psiOff psiOff 0.0 Offset X-Axis Rotation.
 -thetaOff thetaOff 0.0 Offset Y-Axis Rotation.
 -phiOff phiOff 0.0 Offset Z-Axis Rotation.
Reference Da and Dr Values:
 -daRef daRef 0.0 Reference Da Value.
 -drRef drRef 0.0 Reference Dr Value.
 -rhRef rhRef 0.0 Reference Rh Value.
Reference Angles for Simultaneous Tensor Fitting:
 -psiRef psiRef 0.0 Reference X-Axis Rotation.
 -thetaRef thetaRef 0.0 Reference Y-Axis Rotation.
 -phiRef phiRef 0.0 Reference Z-Axis Rotation.
 -norotref No Rotations (Default).
 -rotref Use Reference Rotations. Sets Default Angles to Zero.
Extraction of Da, Dr Etc (for -svd and -saupe):
 -euler Solve for Euler Angles, Da, Dr (Default).
 -noeuler Don't Solve for Euler Angles.
Associated Force Constant Scale:
 -fc 1.0 Force Constant Scale.
  This stand-alone program uses the same facilities as the DYNAMO functions dynSimulate -cs and dynSimulate -dc.

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