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: Jul 24, 2011 / Webmaster