NAME
     nmrDraw - Graphics Interface for NMR Processing and Analysis

SYNOPSIS
     nmrDraw [-in inName] [-dir dirName] [-file  fileExp]  [-name
     defName] [-text textDir] [-read] [-cellX xPix] [-cellY yPix]
     [-type1 small | medium | large] [-type2  small  |  medium  |
     large]  [-square]  [-focus]  [-track]  [-scroll]  [-repaint]
     [-norepaint]  [-frp  repaintCount]  [-dbg]  [-verb]  [-draw]
     [-clear]  [-frzLevels  Always | Sometimes | Never] [-frzZoom
     Always | Sometimes  |  Never]  [-autoScale]  [-grid]  [-pix]
     [-image]  [-peak]  [-vert]  [-zero]  [-cursor]]  [-relative]
     [-compress] [-iz zPlane] [-ia aPlane] [-func  fnTab]  [-proc
     scriptName]  [-nosys] [-zfht] [-mult contFactor] [-plev num-
     Levels] [-nlev numLevels]] [-hi firstHeight] [-plot 1 | 2  |
     3]  [-pcc  numColors]  [-pHue1  hue]  [-pHue2  hue]  [-pSat1
     saturation]  [-pSat2  saturation]  [-pVal1  value]   [-pVal2
     value]  [-ncc  numColors] [-nHue1 hue] [-nHue2 hue]] [-nSat1
     saturation]  [-nSat2  saturation]  [-nVal1  value]   [-nVal2
     value]  [-XOR  Always  |  Sometimes | Never] [-virt Always |
     Sometimes | Never] [-labMode Normal | XOR | Overlay] [-svri]
     [-colors clrList] [-color0 zeroClr] [-color1 1dClr] [-colorC
     cClr]  [-colorG  gridClr]  [-colorX  xClr]]  [-colorY  yClr]
     [-colorZ zClr] [-colorA aClr] [-colorL lClr] [-colorE eClr]]
     [xviewFlags]

SPECIAL NOTE
     This manual page is under development.

DESCRIPTION
     NMRDraw is  a  User-oriented  X11  graphical  interface  for
     inspecting  and  processing  multidimensional  NMR data.  It
     works in conjunction with the nmrPipe program  for  spectral
     processing via UNIX pipes.

     In its current implementation, NMRDraw is  used  to  prepare
     data  for use with computer-assisted analysis and assignment
     programs  such  as  PIPP  (Dan  Garrett,  NIH),  ANSIG  (Per
     Kraulis,  Karolinska  Institute), or NMRView (Bruce Johnson,
     Merck Pharmaceutical).  NMRDraw facilities include:

         Display of 2D Planes from  either  processed  or  unpro-
         cessed  multidimensional data, including interactive and
         User-specified 2D Zoom, adjustable  color  schemes,  and
         viewing  of  the  next  2D plane in a series by a single
         mouse click.

         Real-time display of one or more 1D slices  superimposed
         over  2D  spectral graphics, with interactive adjustment
         of zoom region, vertical scale, and vertical offset.


         Interactive processing of 1D slices from  any  dimension
         of a spectrum, as well as automatic processing according
         to pre-defined schemes.

         Real-time phase correction of  one  or  more  1D  slices
         simultaneously,  with  coarse and fine phase adjustment,
         interactive pivot point selection, and automatic  recon-
         struction of imaginary data when needed.

         An nmrPipe shell-script editor,  for  creating,  saving,
         and executing multidimensional conversion and processing
         schemes.

         Interactive adjustment of chemical shift calibration.

         Color and monochrome PostScript hard copy  plot  genera-
         tion.

     Other extraction, display, and analysis facilities,  includ-
     ing projections, graphics overlays from one or more spectra,
     and automated/interactive  peak  picking,  are  included  or
     under development.

A TYPICAL SESSION WITH NMRDRAW
     There  are  many  possible  scenarios  for  a  session  with
     NMRDraw;  a  typical session for processing and inspecting a
     3D spectrum might include the following steps:

         Use the NMRDraw Macro Edit facility to create, save, and
         execute  a  UNIX  shell-script  which converts an unpro-
         cessed spectrometer format data file to an nmrPipe  for-
         mat data file.

         Read and display the converted, unprocessed  data  file;
         inspect  the raw data to see whether it was acquired and
         converted successfully.

         Interactively process a 1D slice  from  the  data  file;
         determine  phase  correction values and other processing
         parameters.

         Create, save and execute a UNIX shell-script to  process
         the  first  2D  plane  from the data, using the interac-
         tively determined processing parameters.

         Read and display the processed plane; evaluate the  need
         for  any additional processing, such as baseline correc-
         tion.

         Create, save, and execute a UNIX shell-script to process
         the  entire  3D  spectrum, incorporating the previous 2D
         scheme.
         Read and display 2D planes, 1D  slices,  etc.  from  the
         processed 3D spectrum.

APPEARANCE OF NMRDRAW
     NMRDraw has several components, which provide  for  informa-
     tional  text,  command  entry,  and  spectral  display.  The
     appearance  and  behavior  of  NMRDraw  can  be  changed  by
     command-line  arguments  and  by  other graphics parameters,
     especially the  configuration  parameters  of  the  graphics
     environment (window manager) being used.  The usual behavior
     of NMRDraw is described here:

         By default, the  NMRDraw  window  takes  up  the  entire
         screen.  The window border at the top edge of the screen
         describes the current functions of the mouse buttons, if
         any.   It  is also sometimes used to display information
         about the current data.

         The command panel, which extends across the top  of  the
         nmrDraw window, contains pull-down menu buttons for com-
         mand entry, numerical  fields  for  specifying  spectral
         locations  and  display  parameters, and slider bars for
         adjusting phase correction  values  interactively.   The
         command panel usually has a gray background.

         The canvas takes up the remaining portion of the nmrDraw
         window; it has a purple background by default.  The can-
         vas contains a rectangular spectral graphics area, where
         displays  such  as  contour  plots  will  be  drawn.  By
         default, this graphics  area  has  a  black  background.
         Many  facilities  of  NMRDraw  make use of the mouse; in
         these cases, the mouse buttons will perform one  set  of
         actions  while  the mouse pointer is inside the spectral
         graphics area, and a different set of actions  when  the
         mouse pointer is to the left or below the graphics area,
         in the purple borders.  As mentioned  above,  the  mouse
         button  functions  will  be  displayed  the  the topmost
         border of the NMRDraw window.

         In addition to NMRDraw's primary  window,  one  or  more
         pop-up  windows may appear during a session.  These win-
         dows are used for special-purpose command entry, such as
         selection  of  the  current  data  file.   More than one
         pop-up may appear on the screen at  a  given  time.   As
         with  NMRDraw's  primary  window,  the  top  border of a
         pop-up will  often  display  useful  information.   Most
         pop-ups  have  a  Done  Button,  which should be used to
         close the pop-up and remove it from  the  screen.   Note
         that  if you remove a pop-up by other means, such as via
         window manager commands, you may not be able to use  the
         pop-up again during the session.

NMRDRAW AND YOUR WINDOW MANAGER
     As noted before, some functions of  NMRDraw  are  under  the
     control of the window manager, the program which coordinates
     the display of multiple windows on the screen.   The  window
     manager  controls  the  behavior of the keyboard, mouse but-
     tons, and window borders.  It also controls  default  place-
     ment  of  windows  on the screen, and the details of moving,
     re-sizing, iconifying and restoring windows.   So,  you  may
     wish to investigate or adjust the details of your own window
     environment in order to make the best use of NMRDraw.

     The current version of NMRDraw has been developed  with  the
     XView  Toolkit  V2.0,  for  use with X11R4. It has been used
     most extensively with the twm and OpenLook window  managers.
     In these cases, the following aspects of the window environ-
     ment seem to have the strongest influence  on  the  behavior
     and appearance of NMRDraw:

         Which mouse button is used to view pull-down menus,  and
         which is used to select a command.

         Whether pop-up windows are placed  automatically  or  by
         hand.

         Whether graphics drawn in overlapping or iconified  win-
         dows is discarded or maintained.

         The colors and fonts used for window borders, etc.

RUNNING AND EXITING NMRDRAW
     In the usual installation, the NMRDraw program can be run by
     typing the command:

        nmrDraw

     This command executes  the  UNIX  shell-script  file  called
     nmrDraw,  which  in  turn  runs the program itself, which is
     called nmrdraw.  You can customize many aspects  of  NMRDraw
     by  editing a version of the nmrDraw shell-script, to change
     the various arguments used to invoke the program.

     You can also  include  arguments  directly  on  the  NMRDraw
     command-line.  For instance, as a short-cut, you can specify
     the default data directory or data name:

        nmrDraw -dir ft -name test%03d.ft3


     In order to exit the NMRDraw program,  you  can  select  the
     Quit  NMRDraw  command  from the NMRDraw File Menu.  You can
     also exit the program by moving the mouse pointer  into  the
     spectral   graphics   area   and   typing  the  character  Q
     (upper-case Q) at the keyboard.

ENTERING COMMANDS IN NMRDRAW
     NMRDraw is operated by a combination of commands entered via
     the  mouse  and  keyboard.  Many commands and parameters are
     selected by using the mouse  with  graphical  items  on  the
     screen; the general nature of some common graphical items is
     described in more detail below.

     The primary commands are selected via Menu  Buttons  in  the
     command  panel.  For instance, the command to draw a contour
     plot on the screen is listed under the Draw pop-up  menu  as
     "d)  Contours",  and  can  be selected via the mouse.  As an
     alternative, the command can be selected from  the  keyboard
     without  the  need to use the mouse.  In this case, the com-
     mand can be selected by typing d (lower-case  d),  as  indi-
     cated at the beginning of the Command Text.

     You can only type commands from the keyboard if the keyboard
     focus  is set to the spectral graphics area.  This generally
     means that the mouse pointer  will  have  to  be  positioned
     inside  the  graphics area before commands are entered.  The
     outer edge of the graphics area will usually be hilighted to
     indicate that commands can be entered.  You can restore key-
     board focus at any time by moving the mouse pointer out  of,
     then back in to, the graphics area.

SOME GRAPHICAL COMMAND ITEMS
     Buttons
          Buttons are graphical items intended to resemble actual
          push-buttons  with  rounded  edges.  They  are  used to
          display a single command or command choice.  To  select
          a Button's command, point to the Button with the mouse,
          and click the left mouse-button.

          Example: most pop-up windows have a Done Button,  which
          can  be used to close the pop-up and remove it from the
          screen.

     Menu Buttons
          Menu Buttons are special Buttons which cause  a  pop-up
          menu  of additional options to be displayed.  Menu But-
          tons look like ordinary Buttons, but they also  include
          a  triangular  caret symbol after the button text; this
          caret signifies that there is a  menu  associated  with
          the  button.  To view the pop-up menu associated with a
          Menu Button, press and hold the right mouse-button; the
          menu  will  appear, and will stay on the screen as long
          as the mouse-button is held.  Command  options  in  the
          pop-up  menu  can  be selected by dragging the mouse to
          highlight the desired option, then releasing the mouse.

          The first command entry in any given menu is called the
          default  command.  The menus are often arranged so this
          default  command  is  a  commonly  used  one.    As   a
          short-cut,  it  is possible to select this default com-
          mand without the need to pop-up the menu.  To do  this,
          use  the  left mouse-button (to select the default com-
          mand) rather than the right mouse-button (used to  make
          the pop-up menu appear).  In this respect, Menu Buttons
          behave  like   ordinary   Buttons,   since   the   left
          mouse-button  is  used  in  both  cases  to  select the
          Button's command.

          Example: the NMRDraw Command Panel includes  Menu  But-
          tons  marked  File,  Draw, and Mouse.  The default com-
          mands for these menus are  the  often-used  options  to
          read a file, draw a contour plot, and view 1D slices.

     Character Text Item
          Character Text Items are one-line regions on the screen
          used  for entering text information such as a file name
          from the keyboard.  Text Items  have  a  label  on  the
          left-hand  side,  followed  by  a horizontal line where
          text typed from the keyboard will be entered.  In order
          to  enter text into a Text Item, point to the item with
          the mouse and click the left mouse-button before typing
          from  the keyboard.  In some cases, entering a carriage
          return at the end of the input line will cause  NMRDraw
          to perform some action related to the input text.

          Example: the Select File pop-up  window  includes  Text
          Items  which  are used to specify the current data file
          and directory; these text items are labeled "File:" and
          "Directory:".   Typing a file name in the "File:" field
          followed by a carriage return  will  cause  NMRDraw  to
          read the specified file.

     Floating-Point Text Item
          Floating-Point Text Items look the  same  as  character
          text  items,  but  they  are used specifically to enter
          floating-point   numbers.     They    will    have    a
          floating-point number as a default value.

          Example: the command panel includes floating-point text
          items  labeled  "P0:"  and  "P1:";  these  are  used to
          display or change the current phase correction values.

     Integer Text Item
          Integer Text Items look  the  same  as  character  text
          items,  but  they  also  include a pair of square caret
          buttons to the right of the one-line  text  field.   As
          the  name  implies,  the  integer text item is used for
          entering an integer value; the  caret  buttons  can  be
          used  to  increment  or  decrement  the current integer
          value.

          Example: the command panel includes integer text fields
          labeled "X:", "Y:", "Z:", and "A:", used for displaying
          or setting the point locations of 1D and 2D data  being
          displayed.

     Slider Bar
          Slider bars are used for interactive  specification  of
          some continuous value, for instance zero or first order
          phase.  Slider bars have the appearance of a  rectangu-
          lar  button  in  a  vertical or horizontal groove.  The
          value associated with  a  Slider  can  be  adjusted  by
          pointing  to  the  Slider's Button with the mouse, then
          dragging the mouse with the left mouse-button  pressed.
          In  addition, you can increment or decrement the slider
          value by clicking left mouse-button while  pointing  to
          either end of the Slider bar groove.

          Example: the command panel includes a  pair  of  slider
          bars marked "P0:" for coarse and fine zero-order phase,
          and a second pair of slider bars marked "P1:" for first
          order phase.

     Edit Window
          An  Edit  Window  is  a  rectangular  region  used  for
          displaying  or  editing  lines  of text.  You can enter
          text at a particular position in the  window  by  first
          pointing  to  that position with the mouse and clicking
          the left mouse-button, then typing  text  at  the  key-
          board.   In  addition,  pressing  and holding the right
          mouse-button in an Edit Window  will  create  a  pop-up
          menu  of  text editing options, which allow you to read
          or save text files, cut and paste text selections,  and
          so on.

          Example: the command Macro Edit in the File  Menu  will
          create  a  pop-up which includes a light-blue Edit Win-
          dow, used for creating UNIX shell-scripts that do spec-
          tral processing.

THE COMMAND PANEL
     The command  panel  contains  several  graphical  items  for
     adjusting commonly-used parameters.  An outline of the func-
     tions of these items follows:

     X:   Use this to increment, decrement, or select a  particu-
          lar  1D slice when viewing 1D slices from the X-Axis of
          the current data.

     Y:   Use  this  to  increment,  decrement,   or   select   a
          particular  1D  slice  when  viewing 1D slices from the
          Y-Axis of the current data.

     Z:   Use this to increment, decrement, or select a  particu-
          lar  Z-Axis  plane.   Under default settings, the plane
          will be automatically read and drawn with the  previous
          zoom region and contour settings.  This option requires
          selection of data as a 3D or 4D template.

     A:   Use this to increment, decrement, or select a  particu-
          lar  A-Axis  coordinate.  Under default settings, a new
          plane will be automatically read  and  drawn  with  the
          previous zoom region and contour settings.  This option
          requires selection of data as 4D template.

     Plus:
          Use this to change the number of positive contour  lev-
          els to use the next time the data is drawn.

     Minus:
          Use this to change the number of negative contour  lev-
          els to use the next time the data is drawn.

     First:
          Use this to select the height of the first contour used
          the  next  time  the  data is drawn.  Negative contours
          will begin at the negative of this height.

     Factor:
          Use this to select the spacing factor between  adjacent
          contours used the next time the data is drawn.

     (+)  Use this button to increment the first  contour  height
          used the next time the data is drawn.

     (-)  Use this button to decrement the first  contour  height
          used the next time the data is drawn.

     P0: (Sliders)
          These sliders control the coarse  and  fine  zero-order
          phase  applied  at  the  selected  pivot  point  of the
          current 1D spectra.  These sliders will only work if  a
          1D  slice is selected, and the Phasing Toggle button is
          ON.

     P1: (Sliders)
          These sliders control the coarse and  fine  first-order
          phase correction.  These sliders will only work if a 1D
          slice is selected, and the Phasing Toggle button is ON.

     P0: (Text)
          Displays or changes the current P0  phase  value;  this
          value  can  be used directly with nmrPipe regardless of
          the pivot setting.

     P1: (Text)
          Displays or changes the current P1  phase  value;  this
          value  can  be used directly with nmrPipe regardless of
          the pivot setting.

     Pivot:
          Displays or changes the position of the phasing  pivot.
          The  pivot  position can also be selected via the mouse
          when viewing 1D slices.

     Phasing Toggle
          This toggle button must be set to ON in order to  apply
          phasing  to  the current 1D data.  But, once the toggle
          is turned ON,  the  current  1D  spectra  will  not  be
          rephased until a slider or phase value is adjusted.

THE FILE MENU
     The File Menu includes commands to select the spectral  data
     of  interest,  as  well  as  commands to read or re-read the
     selected data.  It also includes commands for  creating  and
     modifying  other kinds of files, such as UNIX shell-scripts.
     Importantly, the File Menu includes the command used to Exit
     from NMRDraw.

     Read This command reads a 2D file plane into NMRDraw's  data
          memory;  depending on the 2D Settings, a 2D plot of the
          plane may be drawn automatically once the data is read.
          The name of the data to read is specified by the Select
          File command in the File Menu; 1D and 2D data sets  are
          selected according to their file names, while 3D and 4D
          data are selected according to their template names. In
          the case of 3D and 4D data, the Z-Axis and A-Axis loca-
          tions for the plane to read are taken from the  Z:  and
          A: fields in the command panel.

     Select File
          This command is used to specify the  file  or  template
          name  of  the  spectral data to read.  Select 1D and 2D
          data according to their file names.  Select 3D  and  4D
          data according to their template names.

     Read Only
          This command is similar to the Read command in the File
          Menu,  however  it  will  not  cause any graphics to be
          drawn regardless of other settings.  Use  this  command
          if  you  would  like  to  adjust the display parameters
          before a plot is drawn.

     Previous Data
          This command will read the previous data file.   It  is
          commonly  used to switch between orthogonal planes of a
          3D dataset, as created by commands in the 1D Menu.

     Parameters
          This  command  displays  the  file  parameters  of  the
          current  spectral  data.  The parameter listing is gen-
          erated by the program showhdr;, it is displayed in  the
          Info Window, which will pop up automatically.

     Calibrate PPM
          Provides a pop-up to re-calibrate the  chemical  shifts
          of any axis in the current data:

             1. Change the axis selection,  axis  label,  or  any
             other parameter which needs to be adjusted.

             3. Enter the PPM value for the selected  point;  the
             default point will be set according to the positions
             of the last 1D slices being viewed.

             4. Use the "Apply" button to re-calculate the chemi-
             cal shifts according to the new parameters.

             5. Use the "Save" button to write the  new  calibra-
             tion data.

     Macro Edit
          This  command  is  used  to  create  and  execute  UNIX
          shell-scripts  for  spectral processing.  It provides a
          point-and-click text editor augmented with a series  of
          predefined  conversion and processing scripts.  It also
          allows edited scripts to be saved on the disk and  exe-
          cuted.   Note  that  this  command  could use much more
          documentation here.

     Hard Copy Plot
          This command creates simple  PostScript  plots  of  the
          current  data,  and  optionally  sends  the  plots to a
          printer queue.  The plots are  generated  according  to
          the  current  display  settings  such  as first contour
          height, number of contour levels, etc.

     Info Window
          This command pops up the Info Window,  a  text  editing
          window  used  for  displaying  information such as file
          parameters.

     Quit NMRDraw
          This command exits the NMRDraw program; no confirmation
          to exit is requested.

THE DRAW MENU
     Contours
          Draws a 2D contour plot of  the  current  data  on  the
          screen, using the current contour settings.

     PixMap
          Draws a 2D pixmap of the current data  on  the  screen,
          using  the current contour settings.  It is used as the
          default mode  for  drawing  mixed  time-frequency  mode
          planes.

     Dot Plot
          Draws a 2D dotplot of the current data.  The dotplot is
          a display which shows intensity as a varying density of
          dots.  It is used  as  the  default  mode  for  drawing
          time-domain data planes.

     Clear Graphics
          Erases the spectrum in the graphics area.

     Erase Screen
          Erases the entire screen, both inside and  outside  the
          graphics area.

     2D Full
          Restores the full view of the current data plane.

     2D Toggle
          Toggles the 2D display on or off by changing the color-
          map.

     2D Colors
          Provides a pop-up for adjusting  the  range  of  colors
          used to display positive and negative data.

     Estimate Noise
          Estimates the standard deviation of the spectral noise,
          and resets the first contour height  accordingly.  Note
          that the estimate may be crude.

     2D Limits
          Provides a pop-up for selecting a data region in  spec-
          tral units such as PPM.

     2D Settings
          Provides a pop-up for selecting various 2D drawing pro-
          perties, such as whether or not to use grid lines.

THE MOUSE MENU
     The Mouse Menu provides a list of functions  that  are  per-
     formed  interactively with the mouse, such as extracting and
     drawing 1D slices from the current data.  Whenever the mouse
     is  active,  the  topmost  border of nmrDraw will report the
     functions of the mouse buttons.  The  buttons  perform  dif-
     ferent  actions  depending  on  whether the mouse pointer is
     inside the spectral graphics region, or outside in the  pur-
     ple borders.

     When a given slice is extracted with one of the  Mouse  Menu
     commands, several other commands can be used on it:

        It can be kept on the screen with other 1D  slices  using
        the Append 1D command in the 1D Menu.

        It can be phase corrected interactively using  the  tools
        in the command panel.

        It can be processed or  inverse-processed  using  NMRPipe
        Command or Auto-Process 1D in the Proc Menu

        1D Horizontal
             Real-time extraction of 1D slices from the  horizon-
             tal  axis  of  the current display.  Mouse functions
             allow real-time vertical offset  and  scale  adjust-
             ment, and graphical selection of phase pivot.

        1D Vertical
             Real-time extraction of 1D slices from the  vertical
             axis  of the current display.  Mouse functions allow
             real-time vertical offset and scale adjustment,  and
             graphical selection of phase pivot.

        1D Both
             Real-time extraction of 1D slices from both the hor-
             izontal  and vertical axis of the current display at
             the same  time.   Mouse  functions  allow  real-time
             vertical  offset and scale adjustment, and graphical
             selection of phase pivot.

        1D Z-Axis
             Extraction of individual 1D slices  from  along  the
             Z-Axis of the current display.  This requires that a
             3D or 4D data template is selected.

        1D A-Axis
             Extraction of individual 1D slices  from  along  the
             Z-Axis of the current display.  This requires that a
             4D data template is selected.

        2D Location
             Real-time  display  of  cursor  location   and   the
             corresponding  data value.  Information is displayed
             in the topmost border of nmrDraw.

        1D Zoom
             Provides a zoom-box for selecting  and  expanding  a
             region of the current 1D slice being displayed.

        2D Zoom
             Provides a zoom-box for selecting  and  expanding  a
             region of the current 2D plane being displayed.

        Exit Mode
             Turns off the current mouse function.

THE 1D MENU
     The 1D Menu contains some commands which effect or relate to
     the 1D data being viewed.

     Append 1D
          Appends the current 1D slice  to  the  list  of  slices
          which  will  be kept on the screen.  This allows two or
          more slices to be viewed at the same time.

     Delete 1D
          Deletes all the 1D slices being viewed from the screen.

     1D Full
          Restores the full view of the current 1D slice.

     1D Toggle
          Toggles the 1D display on and off.

     Extract 2D H
          (3D Data Only) Extracts the orthogonal 2D  plane  which
          corresponds   to  the  horizontal  1D  slice  currently
          selected.  The 2D plane will be  extracted  as  a  file
          called  "ext.dat".  The File Menu command Previous Data
          can be used to return to the original 3D data.

     Extract 2D V
          (3D Data Only) Extracts the orthogonal 2D  plane  which
          corresponds   to   the   vertical  1D  slice  currently
          selected.  The 2D plane will be  extracted  as  a  file
          called  "ext.dat".  The File Menu command Previous Data
          can be used to return to the original 3D data.

     Axis Toggle
          Toggles the 1D axis display on and off.

     1D Settings
          Provides a pop-up which adjusts the  properties  of  1D
          displays,   including   whether   the   zero-level   is
          displayed.


THE PEAK MENU
     The Peak Menu provides commands for automated  and  interac-
     tive  peak  detection  in 1D-4D data.  The peak detection is
     actually performed in the background by the nmrWish program.
     The commands in the peak menu are as follows:

     Peak Detection
          Activated the Peak Detection pop-up window.   Use  this
          window  to view and adjust peak detection settings, and
          to execute automated peak detect commands.

     Draw Labels
          Re-draws the peak labels; you can also use the

     Erase Labels
          Erases the peak labels; you can also use the

     Peak Edit
          Enters peak editing mode, described below.

THE PEAK DETECTION POP-UP
     Peak Table:
          Specifies the file name of the peak table  to  read  or
          write.

     Labels:
          Specifies what information is  displayed  by  the  peak
          labels.   There  is a pull-down menu to the right which
          lists the options.  Note that  peaks  which  have  been
          identified as noise are always labeled with asterisks.

     Read Reads the specified peak table;  the  peak  table  must
          already  exist, and should have point coordinates which
          correspond to the current spectrum.

     Write
          Writes the current peak table from memory to a file.

     Clear
          Delete the current peak table in memory.

     Edit This enables  simple  editing  of  the  peak  table  in
          memory.   In  this  version,  there  must  already be a
          current peak table, either  from  "Read"  or  "Detect".
          When  the  "Edit"  option is selected, the mouse can be
          used to insert, delete, or modify peak parameters.   As
          with  other mouse modes, the mouse button functions are
          given in the top border of nmrDraw.  Once a peak  table
          is edited, it should be saved using the "Write" option.

          In the peak  editing  mode,  the  [Left]  mouse  button
          inserts  a  peak, the [Middle] mouse button can be used
          to adjust a peak value, and the  [Right]  mouse  button
          will delete the nearest peak.

          When using the middle mouse button  to  adjust  a  peak
          value, the value to be adjusted is the one selected for
          the label.  This can be changed by the "Labels"  option
          above.   For  example, if the assignment value "ASS" is
          selected for the label, you  can  modify  the  recorded
          assignment.

          After clicking the middle mouse button over the peak to
          change,  type  in the new value followed by the <enter>
          key.  Because of keyboard focus issues, you may have to
          move  the  mouse in and out of the graphics area before
          typing; using the -focus option  of  nmrDraw  may  help
          this.


     Dimensions:
          Sets the number of dimensions for the peak detection.

     Settings ...
          Activates the "Peak  Detection  Settings"  pop-up,  for
          specification of detection parameters described below.

     Detect
          Select this button to detect  peaks  according  to  the
          current  settings.   This will be performed by creating
          and executing a new peak detection script  "pk.tcl"  in
          the  current directory.  Therefore, peak detection will
          only work if you  have  access  permissions  to  create
          files in the current directory.

     Done Use this button to dismiss the "Peak Detection"  pop-up
          window.

PEAK DETECTION SETTINGS POP-UP
     Filter Command:
          The name of a command to execute after peak  detection;
          when  executed,  the  command will be given the name of
          the current peak  table  as  its  last  argument.   The
          intent  of this option is to allow special filtering of
          the  peak  table.   For  example,  using  the   command
          "pkFilter.tcl"  will generate a "simple" version of the
          peak table from the original one.

     Chi2 Threshold:
          This is a probability threshold for noise  peak  rejec-
          tion by chi-square test.  The chi-square test estimates
          the probability that the  sum-of-squares  intensity  in
          the peak's neighborhood could be caused by random noise
          alone.  To use this test, you must enter  a  reasonable
          "Noise:"  value  above.   Increasing the chi2 threshold
          increase the rejection of peaks near the  noise  level.
          If  the  value  is set to one or zero, no peaks will be
          rejected.

     Noise:
          Enter an estimate of  the  standard  deviation  of  the
          spectral  noise  here.  The default value comes from an
          automated estimate.  This  parameter  is  used  in  the
          Chi-squared test to classify random noise peaks.  It is
          also used to estimate errors in peak  position  due  to
          random  noise  (parameters  DX DY DZ and DA in the peak
          table).

     Contour:
          Specifies the minimum number of  contour  levels  which
          define  the  "High:"  and  "Low:" peak detection thres-
          holds.

     High:
          The  detection  threshold  for  positive   peaks.    By
          default,  it is set to the height of the first positive
          contour level in use when the "Peak  Detection"  pop-up
          window appears.

     Low: The  detection  threshold  for  negative   peaks.    By
          default,  it is set to the height of the first negative
          contour level in use when the "Peak  Detection"  pop-up
          window  appears.  If want want to detect positive peaks
          only, set this parameter to a large negative number.

     DDX: ...
          Size of the detection region in +/-  points.   A  given
          point  must  be  larger than all of the other points in
          this detection region in order  to  be  detected  as  a
          peak.

     IDX: ...
          Size of  the  parabolic  interpolation  region  in  +/-
          points.   IncX:  ...  Defines  how much of the spectral
          data is read into memory for peak detection.  Values of
          zero  will  cause the entire spectral region to be read
          at once.  Since some spectral data may be too large for
          this,  it  is  possible  to  perform  peak detection on
          automatically on overlapping regions.  For example,  if
          3D  peak  detection  is  performed  with  a  setting of
          IncX=0, IncY=0, IncZ=16, the  data  will  be  read  and
          analyzed in 16-plane slabs. This will not effect deter-
          mination of peak positions, widths, and  heights,  how-
          ever it can effect the volume (VOL) and bounding region
          values (X1/X3 etc).

     Local Noise:
          By default, the Chi-square noise classification  scheme
          uses  a  uniform  noise  estimate  for all parts of the
          spectrum.  Selecting one of the X Y Z or  A  checkboxes
          will  allow for an adaptive noise estimate with respect
          to the selected dimension.  This  can  help  compensate
          for  noise  ridges.   Special  Options Currently, these
          options select how noise peaks are identified and  han-
          dled:
         Sinc Detect If this option is selected, the peak  detec-
         tion module will attempt to identify peaks which are due
         to truncation noise (sinc artifacts).

         Reject Noise Peaks If this option is selected, any  peak
         classified  as  noise (either random noise or truncation
         noise) will be automatically eliminated  from  the  peak
         table.

     Sinc Detect Parameters
          The peak detection module attempts to identify  trunca-
          tion  artifacts based on the details of window function
          and zero filling which were applied to  each  dimension
          of  the data.  By taking this information into account,
          it is possible to estimate for a  given  peak  how  far
          truncation  wiggles  would  extend  in  each  dimension
          before falling below the  detection  threshold.   XAdj:
          ... In the artifact detection procedure, the height and
          extent of the truncation peaks are modeled as a profile
          which  decreases  as  1/X, where X is the distance from
          the peak center, and in order for a small  peak  to  be
          classified as the truncation artifact of a larger peak,
          the smaller peak must fall  below  the  profile.   This
          value  is  used  as a multiplying factor to increase or
          decrease the overall profile height. XTol: ... In order
          for  a  small  peak  to be classified as the truncation
          artifact of a larger peak, the  two  peaks  must  align
          along  a  given  dimension.   This  value specifies the
          tolerance in points for deciding whether two peaks  are
          aligned.   XLW:  ...  A  rough estimate of the original
          linewidth in Hz in a given dimension before any  window
          function was used.

     Save Script
          Selecting this command will save a new version  of  the
          peak detection script "pk.tcl" without executing it.

     Done Use this button to dismiss  the  "Peak  Detection  Set-
          tings" pop-up window.

PEAK TABLE PARAMETERS
     INDEX
          the unique peak ID number.

     X_AXIS ...
          the position of the peak in points, by parabolic inter-
          polation.

     DX ...
          estimate of the error in peak position  due  to  random
          noise, in points.

     X_PPM ...
          the position of the peak in PPM, by parabolic  interpo-
          lation.

     X_HZ ...
          the position of the peak in Hz, by parabolic interpola-
          tion.

     XW ...
          the full width at half height in points,  estimated  by
          parabolic interpolation.

     XW_HZ ...
          the full width at half height in Hz, estimated by para-
          bolic interpolation.

     X1/X3 ...
          coords of the bounding region surrounding the  peak  or
          its cluster in points.

     HEIGHT
          the peak height, estimated by parabolic interpolation.

     DHEIGHT
          the error peak height due to random noise, estimated by
          parabolic interpolation.

     VOL  the peak volume, estimated as the sum of intensities in
          the neighborhood of the peak maximum.

     ASS  location to hold assignment data.

     PCHI2
          the chi-square probability for the peak (i.e. probabil-
          ity that the peak could be due to random noise alone).

     CLUSTID
          identifies the cluster of peaks that a given peak over-
          laps.  Peaks with the same CLUSTID value are considered
          to be in one overlapped group.

     MEMCNT
          the total number of peaks which are in a  given  peak's
          cluster (i.e. peaks which have the same CLUSTID value).

     TYPE An  integer   describing   the   peak   classification;
          currently  1  =  Peak, 2 = Random Noise, 3 = Truncation
          artifact.

THE PROC MENU
     The Proc Menu provides two ways to process  the  current  1D
     slice, as explained here:

     NMRPipe Command
          Provides  a  pop-up  window  for  executing  individual
          nmrPipe  processing  functions on the current 1D slice.
          To perform processing, enter the  name  of  an  nmrPipe
          function  on  the  given  command  line, along with any
          additional arguments; For instance, "ft -inv" would  be
          the command for inverse Fourier transform. As an alter-
          native to typing the function and  arguments,  a  small
          menu  of  common functions is provided.  Once the func-
          tion is entered, execute the  processing  by  typing  a
          carriage return, or by clicking the Execute button.

     Auto-Process 1D
          This command will execute a pre-defined macro which  is
          responsible  for  processing the current 1D slice.  The
          macro used is specified by  the  command-line  argument
          -proc  in  the  nmrDraw script.  The default version of
          the macro will apply a window, zero  fill,  and  FT  to
          time-domain  data;  if the axis name is "HN", a solvent
          filter and extraction of an amide chemical shift  range
          will also be applied.

          In the case of frequency-domain data, inverse  process-
          ing   will  be  applied,  automatically  restoring  the
          current 1D slice it to its original time-domain form as
          best as possible.

FILE OPTIONS
     -in inName
          Default Input Name, reads data on start-up.

     -dir dirName
          Default input directory.

     -file fileExp
          Expressions for directory list filter.

     -name defName
          Default Input Name, does not read data on start-up.

     -text textDir
          Help Text Directory.

     -read
          Auto-Read on Startup.

GENERAL OPTIONS
     -cellX xPix
          Character Cell Width.

     -cellY yPix
          Character Cell Height.  -type1 size General  specifica-
          tion  for  the  NMRDraw  ordinary  font;  use  keywords
          "small", "medium", "large", or "extraLarge".

     -type2 size
          General specification for the NMRDraw large  font;  use
          keywords "small", "medium", "large", or "extraLarge".

     -square
          Make the spectral graphics area square.

     -track
          When a mouse mode is turned on, the default 1D location
          tracks the mouse.

     -focus
          If this option is used, NMRDraw will attempt to get the
          keyboard focus automatically, making tasks such as peak
          editing easier.

     -scroll
          Use Scrollable Panel.

     -repaint
          Force Manual Repaint Mode.

     -norepaint
          Avoid Manual Repaint Mode.

     -frp First Repaint Count.

     -dbg Debug Message Level.

     -verb
          Toggle Verbose Mode On.

2D DISPLAY OPTIONS
     -draw
          Auto-Draw with Read.

     -clear
          Auto-Clear when Drawing.

     -frzLevels
          Freeze Contour Levels: Always Sometimes Never

     -frzZoom
          Freeze 2D Zoom Region: Always Sometimes Never

     -autoScale
          Auto-Calc Contour Level.

     -grid
          Draw Grid Lines.

     -pix PixMap Display is Default.

     -image
          Image Display Setup.

1D DISPLAY OPTIONS
     -vert
          Enable Vertical Plots.

     -zero
          Draw 1D Zero Level Line.

     -cursor
          Draw 1D Position Cursor.

     -relative
          Relative 1D Scaling.

     -compress
          1D Display Compression.

COORDINATE OPTIONS
     -iz  Z-Plane Number.

     -ia  A-Plane Number.

PROCESSING OPTIONS
     -func fnTab
          Function Table Name.

     -proc script
          Processing script used for automatic 1D processing.

     -nosys
          Suppress system calls.

     -zfht
          Enable temporary zero fill with Hilbert transform.

CONTOUR LEVEL OPTIONS
     -mult contFactor
          Contour Level Factor.

     -plev numLevels
          Number of Positive Levels.

     -nlev numLevels
          Number of Negative Levels.

     -hi firstHeight
          First Contour Height.

2D DRAWING COLOR OPTIONS
     -plot plotMode
          Color mode for hard-copy plots; these will be  selected
          from inside the program in future versions:
            1 = Black and White
            2 = Gray Scale (Not supported yet)
            3 = Color

2D DRAWING COLOR OPTIONS
     -pcc numColors
          Positive Color Count.

     -pHue1 hue
          Positive colors, First Hue [0-1].

     -pHue2 hue
          Positive colors, Last Hue  [0-1].

     -pSat1 saturation
          Positive colors, First Saturation [0-1].

     -pSat2 saturation
          Positive colors, Last Saturation  [0-1].

     -pVal1 value
          Positive colors, First Value [0-1].

     -pVal2 value
          Positive colors, Last Value  [0-1].

     -ncc numColors
          Negative Color Count.

     -nHue1 hue
          Negative colors, First Hue [0-1].

     -nHue2 hue
          Negative colors, Last Hue  [0-1].

     -nSat1 saturation
          Negative colors, First Saturation [0-1].

     -nSat2 saturation
          Negative colors, Last Saturation  [0-1].

     -nVal1 value
          Negative colors, First Value [0-1].

     -nVal2 value
          Negative colors, Last Value  [0-1].

1D/2D OVERLAY DRAWING OPTIONS
     -XOR XOR Drawing Keyword: Always Sometimes Never

     -svri
          Server Image Color Palette.

     -colors clrList
          Color Name List.

     -color0 zeroClr
          Zero Line Color.

     -color1 1dClr
          Active 1D Plot Color.

     -colorC cClr
          Cursor Bar Color.

     -colorG gridClr
          Grid Line Color.

     -colorX xClr
          X-Axis 1D Plot Color.

     -colorY yClr
          Y-Axis 1D Plot Color.

     -colorZ zClr
          Z-Axis 1D Plot Color.

     -colorA aClr
          A-Axis 1D Plot Color.

     -colorL lClr
          Label Color.

     -colorE eClr
          Background Color.

     Color Name Options:

        black        red          orange       yellow
        green        blue         violet       cyan
        magenta      lightGray    dimGray      white

LEGAL NOTICE
     This  program  and  its related software  is  provided   "as
     is".   The  NIH, the Laboratory of Chemical Physics,  NIDDK,
     and  the authors  make  no  warranties,  either  express  or
     implied,   as  to any  matter  whatsoever  with  respect  to
     the  software.  In particular, any and  all  warranties   of
     merchantability   and fitness for any particular purpose are
     expressly excluded.  In no  event will the NIH, the  Labora-
     tory  of  Chemical  Physics, NIDDK, or the authors be liable
     for any loss of  profits,  any  incidental,  special,  exem-
     plary,   or  consequential  damages of any nature whatsoever
     (including  without  limitation, loss of use or  other  com-
     mercial  or  research  loss) arising out  of  or relating to
     the use or performance of the software.