NMRWish Command List dynAlign Calculate Optimal Alignment of Two Structures

Command-Line Argument List

dynAlign: Compare two segments:
 -refSrc rPDB  Reference PDB Name.
 -aSrc   aPDB  Source PDB Name.
 -r1     res1  First Residue in Reference Segment.
 -rN     resN  Last Residue in Reference Segment.
 -a1     a1    First Residue in Segment to Compare.
 -apply        Apply Rotation.
 -matrix       Use Distance Matrix Comparison.
 -atom   aList Atom Name List (Default: CA C N).
Rotation Angle Starting Values and Limits:
 -psi      [1.0]     Initial X-Axis Rotation.
 -psiMax   [360.0]   Maximum X-Axis Rotation.
 -psiMin   [-360.0]  Minimum X-Axis Rotation.
 -theta    [1.0]     Initial Y-Axis Rotation.
 -thetaMax [360.0]   Maximum Y-Axis Rotation.
 -thetaMin [-360.0]  Minimum Y-Axis Rotation.
 -phi      [1.0]     Initial Z-Axis Rotation.
 -phiMax   [360.0]   Maximum Z-Axis Rotation.
 -phiMin   [-360.0]  Minimum Z-Axis Rotation.