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
scroll.tcl: On-Screen Strip Plot Manipulation for One or More 3D Spectra.

Flag Argument Default Description
 -tab tabName hn.tab 2D Table for strip locations.
 -in inName ft/test%03d.ft3 ... 3D Spectral data template.
Contour Drawing:
 -hi contHi Auto ... First contour height.
 -plev nPos 10 ... Number of Positive Contours.
 -nlev nNeg 10 ... Number of Negative Contours.
 -mult mult 2.0 ... Factor for Auto contour height.
Analysis Features:
 -pk pkName None ... 3D Peak Table Data.
 -seq seqName None Residue Sequence Table.
 -cs csName None Reference Chemical Shift (CS) Table.
 -csVar csVar SHIFT Reference CS Table Variable Name.
 -pkXVar xVar Auto ... Peak Table X-Axis PPM Variable Name.
 -pkYVar yVar Auto ... Peak Table Y-Axis PPM Variable Name.
 -pkZVar zVar Auto ... Peak Table Z-Axis PPM Variable Name.
 -assVar aVar ASS ... Peak Table Assignment Variable Name.
 -xTol xTol 0.03 ... X-Axis Comparison Tolerance, PPM.
 -yTol yTol 0.15 ... Y-Axis Comparison Tolerance, PPM.
 -zTol zTol Auto ... Z-Axis Comparison Tolerance, PPM.
 -cmnd Show Command Panel Window.
Strip Axis Names:
 -xName xName Auto ... First Axis Name of Strip 2D Coord.
 -yName yName Auto ... Second Axis Name of Strip 2D Coord.
 -zName zName Auto ... Axis Name of Strip Dimension.
Strip Spectral Region Widths:
 -xw xw 0.12ppm ... X-Axis +/- Width For view1.
 -yw yw 0.80ppm ... Y-Axis +/- Width For view2.
 -zw zw 1 ... Z-Axis +/- Width For Srip Projection.
Strip Region Limits, ppm, Hz, pts or %:
 -z1 zStart 0% ... Strip Starting Coord.
 -zn zEnd 100% ... Strip Ending Coord.
 -zOff zOff 0.0 ... Z Offset to Apply, PPM.
Coordinate Table Names:
 -xVar xVar Auto Variable name of first 2D PPM coord.
 -yVar yVar Auto Variable name of second 2D PPM coord.
 -idVar idVar INDEX 2D Location Table ID Variable Name.
 -xOff xOff 0.0 ... X Offset to Apply, PPM.
 -yOff yOff 0.0 ... Y Offset to Apply, PPM.
Single/Pairwise Strip Plotting
 -view1 Plot First (X-Axis) View For Each 2D Coord (Default).
 -view2 Plot Second (Y-Axis) View For Each 2D Coord.
 -pair Plot Both Complementary Views (same as -view1 -view2).
Strip Labels:
 -lab lVar INDEX Variable name for Strip Label.
 -xGrid Draw X-Axis Grid Line (Default).
 -noxGrid No X-Axis Grid Line.
 -yGrid Draw Y-Axis Grid Lines (Default).
 -noyGrid No Y-Axis Grid Lines.
Colors:
 -fg fgC yellow ... Strip Foreground (Border) Color.
 -bg bgC black Strip Background Color.
 -colorF fC gray20 ... Folded Background Color (Or Keyword 'Blank').
 -colorA aC white Axis and Info Text Color.
 -colorH aH white Hilight Color for Active Items.
 -colorG gC dimGray Strip Grid Color.
 -colorW wC gray20 Viewer Window Color.
 -colorL lC white ... Label Color.
 -colorP pC Multi ... Positive Contour Color.
 -colorN nC Multi ... Negative Contour Color.
 -colorC cC Default ... Cursor Colors.
 -colorQ cQ white ... Cursor Label Colors.
Strip Graphic Region Widths:
 -dx xwPix 40 Strip Width, Pixels.
 -qx1 xwPix 3 Spacing Between Views, Pixels.
 -qx2 xwPix 6 Spacing Between Spectra, Pixels.
 -qx3 xwPix 9 Spacing Between Groups, Pixels.
 -ySize ywPix Auto Height of Graphics Area, Pixels.
Window Geometry:
 -g geom Auto Initial Window Geometry.
 -xAdj xAdj 25 X Adjustment for Window Size, Pixels.
 -yAdj yAdj 70 Y Adjustment for Window Size, Pixels.
 -cAdj cAdj 220 X Adjustment for Command Panel Window.
 -cx cx 12 X Character Size, Pixels.
 -cy cy 15 Y Character Size, Pixels.
Special Options:
 -history hName None File for Recording Strip Order Adjustments.
 -cursors nC 0 ... Number of Horizontal Tracking Cursors.
 -shade Shade Backgrounds for Folded Data.
 -noshade No Shading of Backgrounds for Folded Data.
 -link Communicate to Other Scroll Applictions.

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last updated: Apr 20, 2011 / big frank

Contact site designer mimi at mdelaglio@hotmail.com