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
mfr2torsion.tcl: Extract Named Torsion Restraints from MFR Search Results.

Flag Argument Default Description
 -mfr mfrName mfr.tab Input Fragment Table.
 -ref pdbName ext.pdb PDB File Reference Input.
 -out pdbName mfrTor.pdb PDB File Output.
 -r1 r1 First First Residue in Output Range.
 -rN rN Last Last Residue in Output Range.
 -skip skip 1 Head/Tail Residues to Skip.
 -maxPhi mPhi 60.0 Max Allowed Phi Std Deviation.
 -maxPsi mPsi 60.0 Max Allowed Psi Std Deviation.
Clusters and Cluster Scoring (N = Cluster Member Count):
 -wInfo wPairs TOTAL_Q 1.0 Weight Coefficients for Score.
 -dPhi dPhi 30.0 Phi Nearest Neighbor Distance.
 -dPsi dPsi 30.0 Psi Nearest Neighbor Distance.
 -useNScale Scale Scores by Sqrt(N) (Default).
 -noNScale No Member Count Scaling of Score.
Fragments to Use:
 -dcNMin dcNMin 15 Minimum Allowable DC Values.
 -maxRank maxRank 10 Max Rank of Fragments.
Source of Input Structures:
 -pdbDir pdbDir PDBH_DIR Location of MFR PDB Files.
 -fragDir fragDir None Location of MFR PDB Fragments.
 -useFragName Use FRAG_NAME from MFR Table.

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last updated: Apr 20, 2011 / big frank

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