Frank Delaglio, Ph.D.

19804 Maycrest Way
Germantown MD 20876 USA

301 806-0867
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.