Frank Delaglio, Ph.D.

19804 Maycrest Way
Germantown MD 20876 USA

301 806-0867
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.