Welcome: an Introduction to this Site
NMRPipe: a Comprehensive Software System for Biomolecular NMR
Special Applications: NMR Drug Screening, Automation, and so on
Dipolar Couplings, Chemical Shifts, and Protein Structure
Miscellaneous

Frank's CV, Recent Slides, and Thesis

 

  

 

  Frank Delaglio, Ph.D.

   Software Science Consultant
  13840 Grey Colt Drive
  North Potomac MD 20878 USA

  Tel: 301 806-0867
  Fax: 301 309-8717
  E-mail: delaglio@nmrscience.com



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.
Notes:
  This stand-alone program uses the same facilities as the DYNAMO functions dynSimulate -cs and dynSimulate -dc.

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last updated: Jan 22, 2009 / big frank

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