Scripts of the NMRPipe System
scroll.tcl: On-Screen Strip Plot Manipulation for One or More 3D Spectra.

Flag Argument Default Description
 -tab tabName 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.
 -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: Jul 24, 2011 / Webmaster