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
pdb2ac.tcl: Create DYNAMO atomic coord (AC) restraint table from PDB.

Flag Argument Default Description
 -in pdbName ref.pdb PDB Input for Coords.
 -ref seqName None PDB Input for Sequence (If Different).
 -r1 r1 First First Residue for Sequence PDB.
 -rN rN Last Last Residue for Sequence PDB.
 -a1 a1 r1 First Residue for Coord PDB.
 -id id 1 First Index Number for Restraint Output.
 -seg segName PROT Segment Name for Restraint Output.
 -dLo dLo 0.0 Lower Distance Bound.
 -dHi dHi 0.0 Upper Distance Bound.
 -fc fc 10.0 Restraint Force Constant.
 -atom aList C* ... Atom Name List. Default: C* N* O* S* P* F*
 -dx dx 0.0 Additional X-Axis Offset.
 -dy dy 0.0 Additional X-Axis Offset.
 -dz dz 0.0 Additional X-Axis Offset.
 -hetatm Include HETATM entries from PDB Input.
 -nohetatm Ignore HETATM entries (Default).
 -center Center Coords of PDB Input.
 -nocenter No Centering of PDB Input (Default).
 -hdr Print Header in Output (Default).
 -nohdr No Header in Output.
 -na Interpret Sequence for DNA/RNA. Also -dna -rna
 -nona No Adjustment for DNA/RNA (Default).
Coordinate Modes (Use Only One):
 -fixed Fragment Coords are Fixed (Default).
 -nofixed Fragment Can Translate and Rotate.
 -rotfixed Fragment Can Translate Only.
Multiple Fragment Mode (Zero for Single Fragment Mode):
 -segLength sLength 0 Segment Length of Fragments.
 -segStep sStep 0 Offset Between Fragments.
 -equiv Include All Tensor-Equivalent Rotations.
 -excl resList None Starting Res IDs Not to Rotate.
Notes:
  Multiple Fragment Mode Uses '-nofixed' Coordinate Mode by Default.

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last updated: Apr 20, 2011 / big frank

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