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
ipap.tcl: Project Assignments onto IP/AP Peak Tables.

Flag Argument Default Description
 -specName1 specName1 sum.ft2 Input Spectrum 1 (ASS-J/2).
 -specName2 specName2 dif.ft2 Input Spectrum 2 (ASS+J/2).
 -inName1 tabName1 sum.tab Input Peak Table 1.
 -inName2 tabName2 dif.tab Input Peak Table 2.
 -outName1 tabName1 sum.ass.tab Output Peak Table 1.
 -outName2 tabName2 dif.ass.tab Output Peak Table 2.
 -assName assTabName ass.tab Input Assignment Table.
 -ndim dimCount Auto Dimension Count.
 -single Single-Spectrum Mode ON.
Auto-Assign at Start-Up:
 -auto Auto Assign Peaks at Start (Default).
 -noauto No Auto Assign Peaks at Start.
 -nosort No Sort of Assignments at Start.
 -replace Replace All Existing Assignments (Default).
 -noreplace Keep Any Existing Assignments.
Multiplet Description Via Common Offset:
 -jx jxHz 0.0 Expected X-Axis Coupling, Hz
 -jy jyHz 90.0 Expected X-Axis Coupling, Hz
 -jz jzHz 0.0 Expected Z-Axis Coupling, Hz
Multiplet Description Via Individual Peaks:
 -jInfo jList None Offsets for Each Peak, Hz
Assignment Mapping Parameters:
 -xw xwPPM 0.1 X-Axis Region Size for Assignment Mapping, PPM.
 -yw ywPPM 1.0 Y-Axis Region Size for Assignment Mapping, PPM.
 -zw zwPPM 1.0 Z-Axis Region Size for Assignment Mapping, PPM.
 -pk pkN 1 Expected Peak Count in a Spectrum per Assignment.
Drawing Parameters:
 -xv xvPPM 0.15 X-Axis Region Size for Display, PPM.
 -yv yvPPM 2.50 Y-Axis Region Size for Display, PPM.
 -zv zvPts 0 Z-Axis Projection Size for Display, Pts.
 -hi1 hi1 Auto Contour Height for Spectrum 1.
 -hi2 hi2 Auto Contour Height for Spectrum 2.
 -mult mult 7.0 Factor for Auto Contour Height.
Spectrum Colors:
 -color1 c cyan Color for Spectrum 1.
 -color2 c white Color for Spectrum 2.
 -posColor1 c cyan Color for Spectrum 1 (Positive Data).
 -negColor1 c cyan Color for Spectrum 1 (Negative Data).
 -posColor2 c white Color for Spectrum 2 (Positive Data).
 -negColor2 c white Color for Spectrum 2 (Negative Data).
Label Colors:
 -pkOnColor1 c green Color for Current Peaks, Table 1.
 -pkOffColor1 c gray50 Color for Other Peaks, Table 1.
 -pkOnColor2 c green Color for Current Peaks, Table 2.
 -pkOffColor2 c gray50 Color for Other Peaks, Table 2.
 -assOnColor c red Color for Other Assignments.
 -assOffColor c yellow4 Color for Current Assignment.
Spectrum Axis Parameters:
 -xName xName Auto X-Axis Name in Spectrum.
 -yName yName Auto Y-Axis Name in Spectrun.
 -zName zName Auto Z-Axis Name in Spectrum.
Peak Table Parameters:
 -xVar xVar Auto X-Axis Name in Peak Table.
 -yVar yVar Auto Y-Axis Name in Peak Table.
 -zVar zVar Auto Z-Axis Name in Peak Table.
Assignment Table Parameters:
 -xAss xAss Auto X-Axis Name in Assignment Table.
 -yAss yAss Auto Y-Axis Name in Assignment Table.
 -zAss zAss Auto Z-Axis Name in Assignment Table.
 -assVar assV ASS Assignment Name in Assignment Table.
Assignment Table PPM Offsets:
 -xOff xOff 0.0 X-Axis Offset for Assignment, PPM.
 -yOff yOff 0.0 Y-Axis Offset for Assignment, PPM.
 -zOff zOff 0.0 Z-Axis Offset for Assignment, PPM.

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last updated: Jul 4, 2012 / big frank

Contact site designer mimi at mdelaglio@hotmail.com