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
seq2gmc.tcl: Create a DYNAMO Initial/Extended Structure from Sequence Info.


Input Options:
Flag Argument Default Description
 -in tabName csObs.tab Name of Input with DATA SEQUENCE Info.
 -r1 firstRes First First Residue of Input to Use.
 -rN lastRes Last Last Residue of Input to Use.
 -pdb Input is PDB Format.
 -tab Input is Table with DATA SEQUENCE Info (Default).
Input Modes:
 -protein Input is a Protein Sequence.
 -dna Input is a DNA Sequence.
 -rna Input is an RNA Sequence.
 -seqres Use SEQRES Info (-pdb Mode Only). Not implemented yet.
Output Specification:
 -seg segName PROT Output Segment Name (Also: DNA RNA).
 -out outName ext.pdb Name of PDB Extended Structure Output.
 -gmc gmcName ref.gmc GMC Directory Name for Structure.
 -mod modName None GMC Modification Text, if Any.
 -r0 firstRes First Value to Give for Output First ResID.
 -reset Reset Output Segment Name to Blanks.
 -nogmc Don't Create GMC Tables. Creates GMC Sequence Information Only.
Repeated Use for Multiple Segments:
 -cont Sequence Info Will Be Continued.
 -append Append Sequence Info to Existing GMC.
Annealing Options:
 -tInit t 4000 Initial Temperature.
 -initSteps iN 1000 Number of Initialization Steps.
 -highSteps hN 2000 Number of High-Temperature Steps.
 -coolSteps cN 4000 Number of Cooling Steps.
 -print pCount 10 Increment for Report Printing.
 -rasmol rCount 0 Increment for Rasmol Drawing.
 -noext No Simulated Annealing for Extended PDB. Creates GMC Info Random PDB Only (-nosa).
 -novdw No VDW Terms.
 -wireframe Use Rasmol Wrireframe Draw Mode.
Backbone Angle Options (Currently, Protein Only):
 -bb bbName None Start with Backbone Angles from PDB.
 -nohelix Don't Set Final Angles to Helix Values. Backbone Angles will be 'random'.
 -cis Identify cis vs trans Peptide Bonds.
 -nocis All Peptide Bonds are trans (Default).
Special Options:
 -unk resName gly Substitute Name for Unknown Residues.
 -water wCount 0 Number of Water Molecules to Add.
 -frag fLength 0 Homology Fragment Length.
 -offset fOffset 0 Homology Fragment Offset.
 -heme Search for Heme to HIS Connections. Requires PDB Input.
 -disu Search for Disulfide Bonds. Requires PDB Input.

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last updated: Apr 20, 2011 / big frank

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