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
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: Apr 20, 2011 / big frank

Contact site designer mimi at mdelaglio@hotmail.com