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.