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
dynSearch: Perform NMR Homology Search (Molecular Fragment Replacement)

Flag Argument Default Description
 -src pdbSrc PDB Search Target.
 -refName refName Optional Name of PDB Search Target.
Fragment Parameters:
 -segLength segLength Segment Length for Search.
 -scoreCount scoreCount Number of Best Scores to Save.
 -miss missCount Number of Allowed Missing Residues.
NMR Input Parameters:
 -cs csSrc Chemical Shift Table.
 -dc dcSrcList Dipolar Coupling Table List.
 -torsion tSrc Torsion Table.
 -j jSrc J Table.
NMR Homology Score Weights and Parameters:
 -csW csW Chemical Shift Weight.
 -dcW dcW Dipolar Coupling Weight.
 -torsionW tW Torsion Weight.
 -jW jW J Weight (Not Implemented Yet).
 -w wList Dipolar Coupling Residue Weight List.
 -undefFrac uFrac Minimum Fraction of Defined Values.
 -undefW uW Penalty Factor for Undefined Values.
 -ramaThresh rThresh Rama Score Rejection Threshold.
 -csThresh csThresh CS Score Rejection Threshold.
 -csClip csFactor CS Clip Factor in Std Dev for CS.
 -constRMS Use Constant Chemical Shift RMS.
 -wchi Use Weighted Chemical Shifts.
 -nowchi Use Unweighted Shifts (Default).
Dipolar Coupling Tensor Modes (Use Only One Mode):
 -dcSVD SVD Tensor Estimate
 -dcDa Fixed Da for All Tensors.
 -dcDaDr Fixed Da and Dr for All Tensors.
 -dcRh Fixed Rh for All Tensors.
 -dcDaDrRot Fixed Da, Dr, Relative Orientation.
 -retry Number of Retries, Nonlin Tensor Fit.
Residue Homology and Ramachandran Score Parameters:
 -homoW homoW Residue Type Homology Weight.
 -ramaW ramaW Ramachandran Surface Weight.
 -homoMax Use Max for Homology Term.
 -nohomoMax Use Avg for Homology Term.
 -ramaMax Use Max for Rama Term.
 -noramaMax Use Avg for Rama Term.
 -glyOnly Force GLY/GLY matching.
 -noglyOnly GLY matching not required (Default).
 -proOnly Force PRO/PRO matching.
 -noproOnly PRO matching not required (Default).
 -xPRO Use xPRO Definitions (Default).
 -noxPRO No xPRO Definitions.
Use of Backbone Coordinate and Angle RMS Values:
 -rms Calculate BB Coordinate RMS Value.
 -rmsFast Use Faster Coord RMS Approximation.
 -rmsW Backbone Coordinate RMS Weight.
 -phiPsi Calculate BB Angle RMS Value.
 -phiPsiW Phi/Psi Backbone Angle RMS Weight.
Other Arguments:
 -search sPtr Handle from Initialization.
 -pdbName name PDB Name for Current Search.
 -r1 r1 First Residue in Ref Search Range.
 -rN rN Last Residue in Ref Search Range.
 -a1 a1 First Residue in PDB Search Range.
 -aN aN Last Residue in PDB Search Range.
 -out name Output Name for Save Option.
Alternate Fragment and Sequence Source:
 -fragName name Associated Fragment PDB Name.
 -seqName name PDB Source for Sequence Info.
 -seqSrc src PDB Name for Sequence Info.
 -seqOff seqOff ResID Offset for Sequence Info.
Special Modes:
 -init Initialize Search, Return Info Handle.
 -save Save Existing Results.
 -free End Search, Deallocate Data.

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last updated: Apr 20, 2011 / big frank

Contact site designer mimi at mdelaglio@hotmail.com