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



NMRWish Built-In TCL Functions
dynSetTensor: Set the parameters associated with an alignment tensor, as used in dipolar coupling and pseudo-contact shift calculation.

Flag Argument Default Description
 -dc dcSrc DC Table Source.
 -reset Reset Tensor Values to Defaults.
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 and Limits (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 phiMax -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 da 0.0 Reference Da Value.
 -drRef dr 0.0 Reference Dr Value.
 -rhRef rh 0.0 Reference Rh Value.
Reference Angles for Simultaneous Tensor Fitting:
 -psiRef psi 0.0 Reference X-Axis Rotation.
 -thetaRef theta 0.0 Reference Y-Axis Rotation.
 -phiRef phi 0.0 Reference Z-Axis Rotation.
 -norotref No Reference 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 fc 1.0 Force Constant Scale.

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last updated: Apr 20, 2011 / big frank

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