NMRWish Built-In TCL Functions
dynAlign: Find the translation and rotation that minimizes the difference in coordinates between two related molecular structures.

Flag	Argument	Default	Description
`-refSrc`	`rPDB`		Reference PDB Name.
`-aSrc`	`aPDB`		Source PDB Name.
`-r1`	`res1`		First Residue in Reference Segment.
`-rN`	`resN`		Last Residue in Reference Segment.
`-refChain`	`cName`		Chain Name in Reference.
`-refSeg`	`sName`		Seg Name in Reference.
`-a1`	`a1`		First Residue in Target.
`-aChain`	`cName`		Chain Name in Target.
`-aSeg`	`sName`		Seg Name in Target.
`-apply`			Apply Final Rotation/Translation.
`-norot`			Suppress Alignment Rotations.
`-notrans`			Suppress Alignment Translations.
`-fixed`			Suppress Alignment Optimization.
`-phiPsi`			Report Phi/Psi Angle Statistics.
`-list`			List Atom Index Numbers.
`-max`			Report Max Difference with RMSD.
`-map`			Add Distances Onto TEMPFACTOR.
`-matrix`			Use Distance Matrix Comparison.
`-atom`	`aList`		Atom Name List (Default: CA C N).

Rotation Angle Starting Values and Limits:

`-psi`	`psi`	`1.0`	Initial X-Axis Rotation.
`-psiMax`	`psiMax`	`360.0`	Maximum X-Axis Rotation.
`-psiMin`	`psiMin`	`-360.0`	Minimum X-Axis Rotation.
`-theta`	`theta`	`1.0`	Initial Y-Axis Rotation.
`-thetaMax`	`thetaMax`	`360.0`	Maximum Y-Axis Rotation.
`-thetaMin`	`thetaMin`	`-360.0`	Minimum Y-Axis Rotation.
`-phi`	`phi`	`1.0`	Initial Z-Axis Rotation.
`-phiMax`	`phiMax`	`360.0`	Maximum Z-Axis Rotation.
`-phiMin`	`phiMin`	`-360.0`	Minimum Z-Axis Rotation.

Translation Starting Values and Limits:

`-tx`	`tx`	`0.0`	Initial X-Axis Translation.
`-txMax`	`txMax`	`1.0e16`	Maximum X-Axis Translation.
`-txMin`	`txMin`	`-1.0e16`	Minimum X-Axis Translation.
`-ty`	`ty`	`0.0`	Initial Y-Axis Translation.
`-tyMax`	`tyMax`	`1.0e16`	Maximum Y-Axis Translation.
`-tyMin`	`tyMin`	`-1.0e16`	Minimum Y-Axis Translation.
`-tz`	`tz`	`0.0`	Initial Z-Axis Translation.
`-tzMax`	`tzMax`	`1.0e16`	Maximum Z-Axis Translation.
`-tzMin`	`tzMin`	`-1.0e16`	Minimum Z-Axis Translation.

Frank Delaglio, Ph.D.