Welcome: an Introduction to this Site
NMRPipe: a Comprehensive Software System for Biomolecular NMR
Special Applications: NMR Drug Screening, Automation, and so on
Dipolar Couplings, Chemical Shifts, and Protein Structure
Miscellaneous

Frank's CV, Recent Slides, and Thesis

 

  

 

  Frank Delaglio, Ph.D.

   Software Science Consultant
  13840 Grey Colt Drive
  North Potomac MD 20878 USA

  Tel: 301 806-0867
  Fax: 301 309-8717
  E-mail: delaglio@nmrscience.com



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: Jan 22, 2009 / big frank

Contact site designer mimi at mdelaglio@hotmail.com