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:

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.