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



Programs of the NMRPipe System
NMRDraw: Display and Analysis of NMRPipe-Format Spectral Data and Images

Flag Argument Default Description
 -in inName test.ft2 First Input Name.
 -dir dirName . Default Input Directory.
 -file fileExp "*" Directory List Filter.
 -name defName test.ft2 Default Input Name.
 -text textDir . Help Text Directory.
 -read no Auto-Read on Startup.
General Flags:
 -square Square Display Area.
 -track Default Loc Tracks Mouse.
 -focus Allow focus grab.
 -panel Use Stand-Alone Panel.
 -scroll Use Scrollable Panel.
 -verb Verbose Mode On.
 -noverb Verbose Mode Off (Default).
 -noxvwarn XView Warnings OFF (Default).
 -xvwarn XView Warnings ON.
 -dbg 0 Debug Message Level.
2D Display:
 -draw Auto-Draw with Read.
 -clear Auto-Clear when Drawing.
 -frzLevels Sometimes Freeze Contour Levels: Always Sometimes Never
 -frzZoom Sometimes Freeze 2D Zoom Region: Always Sometimes Never
 -autoScale Auto-Calc Contour Level.
 -grid Draw Grid Lines.
 -pix PixMap Display is Default.
 -useTitle Display Title from Header.Window Parameter Set-Up:
 -cellX xPix 0 Character Cell Width.
 -cellY yPix 0 Character Cell Height.
 -xAdj xPix 0 X Width Border Adjustment.
 -yAdj yPix 0 Y Width Border Adjustment.
 -dct msec 1500 Double-Click Time, msec.
 -repaint Force Manual Repaint Mode.
 -norepaint Avoid Manual Repaint Mode (Default).
 -frp 3 First Repaint Count.
 -depth dbits 8 Window Depth. Requires use of the -visual option.
 -type1 size Size for Regular Font: Small Medium Large
 -type2 size Size for Large Font: Small Medium Large
 -visual class Visual Class Keyword: PseudoColor StaticColor StaticGray GrayScale DirectColor TrueColor
  Default (PseudoColor)
Special Application Set-Up:
 -peak filtName Peak Analysis Setup.
 -image Image Display Setup.
 -dev Development Setup.
 -tk Use Tk-Style IPC.
1D Display:
 -lw1d 0 1D Drawing Width, Pixels.
 -vert Enable Vertical Plots.
 -zero Draw 1D Zero Level Line.
 -cursor Draw 1D Position Cursor.
 -relative Use Relative 1D Scaling.
 -compress Use 1D Display Compression.
Coordinates:
 -iz 1 Z-Plane Number.
 -ia 1 A-Plane Number.
Script Execution and External Commands:
 -sh shName csh Command interpreter name.
 -ext extName com File extension for scripts.
 -bin binPath NMRPipe Binary Path.
 -exec execCmnd Command for executing scripts.
 -sys Use System Call Via system().
 -nosys Use System Call Via | csh.
 -fork Use System Call Via fork().
 -save1D Suppress pipeline processing. Use explicit 1D save instead.
Processing:
 -func fnTab func.tab Function Table Name.
 -proc script proc1d.com 1D Processing Script.
 -zfht Temporary Zero Fill (ZF) with Hilbert Transform.
 -nozfht Suppress Temporary ZF with Hilbert Transform. (Default)
Contours:
 -mult contFactor 1.3 Contour Level Factor.
 -plev numLevels 10 Number of Positive Levels.
 -nlev numLevels 10 Number of Negative Levels.
 -hi firstHeight First Contour Height. (Old Option)
 -fhi firstHeight First Contour Height.
 -lhi lastHeight Last Contour Height.
Positive Level HSV Color Vector:
 -pcc numColors 12 Positive Color Count.
 -pHue1 hue 0.5 First Hue, 0.0 to 1.0.
 -pHue2 hue 0.7 Last Hue, 0.0 to 1.0.
 -pSat1 saturation 0.8 First Saturation, 0.0 to 1.0.
 -pSat2 saturation 1.0 Last Saturation, 0.0 t 1.0.
 -pVal1 value 1.0 First Value (Brightness) 0.0 to 1.0.
 -pVal2 value 1.0 Last Value (Brightness) 0.0 to 1.0.
Negative Level HSV Color Vector:
 -ncc numColors 12 Negative Color Count.
 -nHue1 hue 0.5 First Hue, 0.0 to 1.0.
 -nHue2 hue 0.7 Last Hue, 0.0 to 1.0.
 -nSat1 saturation 0.8 First Saturation, 0.0 to 1.0.
 -nSat2 saturation 1.0 Last Saturation, 0.0 to 1.0.
 -nVal1 value 1.0 First Value (Brightness), 0.0 to 1.0.
 -nVal2 value 1.0 Last Value (Brightness), 0.0 to 1.0.
Color Management:
 -XOR Always XOR Drawing Keyword: Always Sometimes Never
 -labMode Normal Label Drawing Keyword: Normal XOR Overlay
 -svri No Server Image Color Palette.
 -virt Never Virtual Colormap Keyword: Always Sometimes Never
 -virtOff 64 Virtual Color Index Offset.
 -static Use Static Color Table.
Program Colors:
 -colors clrList Below Color Name List.
 -color0 zeroClr lightGray Zero Line Color.
 -color1 1dClr yellow Active 1D Plot Color.
 -colorC cClr magenta Cursor Bar Color.
 -colorG gridClr dimGray Grid Line Color.
 -colorX xClr cyan X-Axis 1D Plot Color.
 -colorY yClr red Y-Axis 1D Plot Color.
 -colorZ zClr green Z-Axis 1D Plot Color.
 -colorA aClr orange A-Axis 1D Plot Color.
 -colorL lClr white Axis Label Color.
 -colorP1 p1Clr white Peak Label Color 1D.
 -colorP2 p2Clr white Peak Label Color 2D.
 -colorE eClr black Background Color.
Generic Window Arguments (See also, Output of: nmrDraw -help):
 -size x y Initial NMRDraw Window Width and Height, Pixels.
 -position x y Initial NMRDraw Window Positions, Pixels.
 -geometry geom Initial NMRDraw Window Geometry, X11 style.
Default Color Names:
 black        red          orange       yellow      
 green        blue         violet       cyan        
 magenta      lightGray    dimGray      gray30      
 gray20       white

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last updated: Jan 22, 2009 / big frank

Contact site designer mimi at mdelaglio@hotmail.com