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
  325 Union Avenue #212
  Campbell CA 95008 USA


  Tel: 301 806-0867
  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: Jul 4, 2012 / big frank

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