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
rama.tcl: display and adjust TALOS prediction results.

Directory Settings:
Flag Argument Default Description
 -talosDir mDir . TALOS Main Directory: TALOS_DIR.
 -predDir pDir pred Directory of existing predictions.
 -tabDir tDir tab Subdirectory of TALOS master tables.
Other Options:
 -in inName None Input shifts for predictions.
 -sum sumName pred.tab Prediction summary input/output.
 -ref refName None PDB Reference (for testing).
 -db dbName talos.tab TALOS triplet database file.
 -rand rcName randcoil.tab Random coil shifts table.
 -count mc 10 Max match count per triplet.
 -cols cCount 10 Column Count for Sequence Display.
 -first resID1 First First residue to display.
 -last resIDN Last Last residue to display.
 -sd Display shift distributions.
 -ras Display PDB Reference using RasMol.
 -auto Display predictions in progress.
Examples:
Typical inspection:
  rama.tcl -in ubiq.tab
Inspection when a PDB structure is known:
  rama.tcl -in ubiq.tab -ref ubiq.pdb
Inspection when a PDB structure is known, including Molecular Viewer:
  rama.tcl -in ubiq.tab -ref ubiq.pdb -ras
Display predictions in progress while talos.tcl is running:
  rama.tcl -in ubiq.tab -auto
See also:
  talos.tcl Creates predictions by shift homology.
  vina.tcl Summarize predictions in a single table.
Notes:
  Option -ras requires that RasMol2 is installed and available
  via the command 'rasmol', and that no other instances of RasMol
  are using the screen.
RasMol Reference:
  Roger Sayle and E. James Milner-White.
  RasMol: Biomolecular graphics for all
  Trends in Biochemical Sciences (TIBS),
  September 1995, Vol. 20, No. 9, p. 374.
  http://www.umass.edu/microbio/rasmol

Under Construction

[ Home ] [ Terms of Use ] [ Copyright ]
last updated: Jan 22, 2009 / big frank

Contact site designer mimi at mdelaglio@hotmail.com