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



Scripts of the NMRPipe System
mfr.tcl: MFR: Molecular Fragment Replacement NMR Homology Search.

Flag Argument Default Description
 -segLength fragN 7 Fragment Size, Residues.
 -scoreCount scoreN 10 Number of Fragments to Save.
 -r1 r1 First First Resisue in Search Range.
 -rN rN Last Last Residue in Search Range.
 -ref refName ext.pdb Reference PDB Structure. Used for Sequence.
 -excl eList None List of Proteins Exclude.
Input Tables:
 -dc dcList dObs*.tab Input Dipolar Coupling (DC) Tables.
 -cs csName csObs.tab Input Chemical Shift Table.
 -j jName jcoup.tab Input J-Coupling Table.
 -torsion tName torsions.tab Input Torsion Table.
 -out outName mfr.tab Output Fragment Table.
Weighting Factors:
 -ramaThresh ramaT 0.00 Ramachandran Map Threshold.
 -ramaW ramaW 0.02 Ramachandran Map Weight.
 -dcW dcW 1.00 Dipolar Coupling (DC) Weight.
 -ddcW ddcW 0.00 DC Derivative Weight.
 -jW jW 0.01 J Weight.
 -torW torW 0.05 Torsion Weight.
 -homoW homoW 0.01 Residue Type Homology Weight.
 -rmsW rmsW 0.00 Backbone Coordinate RMS Weight.
 -phiPsiW phiPsiW 0.00 Backbone Angle RMS Weight.
 -alpha expAlpha 3.00 Weight for MFR Da/Dr Estimate.
 -dcN dcNMin 15 Minimum DC Count For Tensor.
 -retry dcRetry 100 Number of Retries, Tensor Fit.
Chemical Shift (CS) Options:
 -csThresh csThresh 3.00 Max Allowable CS Score.
 -csW csW 0.50 Overall CS Score Weight.
 -csWList awList None Atom Name/CS Weight Pair List.
 -csClip csClipF 3.0 CS Clip Factor, in Std Deviations. Use 0.0 for No Clipping.
Dipolar Tensor Calculation Modes:
 -dcSVD Use SVD (Default).
 -dcDa Use Fixed Da.
 -dcDaDr Use Fixed Da and Dr.
 -dcRh Use Fixed Rh (Rh = Dr/Da).
 -dcDaDrRot Use Fixed Da, Dr, Rotation.
Optional Dipolar Coupling Tensor Reference Values:
 -daRef daList Da Values for Each Tensor.
 -drRef drList Dr Values for Each Tensor.
 -rhRef rhList Rh Values for Each Tensor.
Optional Tensor Orientations, Relative to First Tensor:
 -rxRef rxList X Rotation Offsets.
 -ryRef ryList Y Rotation Offsets.
 -rzRef rzList Z Rotation Offsets.
Use of Backbone Coordinate or Angle RMS for Report or Search:
 -rms Report Backbone Coord RMS.
 -phiPsi Report Backbone Angle RMS.
 -rmsFast Fast, Less Accurate Coord RMS.
 -rmsSearch Search by Coord RMS Only.
 -phiPsiSearch Search by Angle RMS Only.
Analysis of Structural Variation Within Group:
 -dist fDist 0.5 Max RMSD Between Similar Fragments.
Database Location:
 -pdbList listName PDBH_TAB List Table of PDB Files.
 -pdbDir pdbDir PDBH_DIR Location of PDB Files.
 -csDir csDir None Optional CS Tables for PDBs.
 -talos Set Above for TALOS Search.
Special Modes for Rescoring MFR Table or Refined Fragments, Resets Default Output Name to mfrScore.tab:
 -rescore mfrInName None MFR Table for Rescore.
 -fragDir fragDir None Directory of Refined Fragments.
 -initDir initDir init Directory of Initial Fragments.
 -useFragName Use FRAG_NAME as PDB Input Name.

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last updated: Jan 22, 2009 / big frank

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