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.

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last updated: Jul 24, 2011 / Webmaster