.noesy.0. The full name must be used when the windows
are referred to using explicit Tcl commands.
To create a new spectral window using the
NMRView GUI choose Add from the Windows entry of the
Control Panel menu bar. The following panel will appear.
- Create
- Click on this to create a new spectral window with the name specified in
the text field of this panel. A new window will be created and the
windowAdd panel will close.
If the name specified is already in use by another spectral
window a new spectral window will be added within the toplevel frame
occupied by the existing window. The new window will be added to the right
of the existing windows, and all the windows will adjust their sizes so that
they equally divide the toplevel window. This only works, however, if the
previous windows in that toplevel were created with the Row and
Column entries set to 1.
- Close
- Click on this entry to close the panel without opening a new window.
A grid of windows can be created within a single toplevel window by
setting the Rows and Columns entries to values greater than
1. For example, to create 6 windows layed out in two rows and three columns
set Rows to 2 and Columns to 3. All the windows will
appear in a single toplevel window.
Spectral windows can also be
created using Tcl commands. The most convenient alternative is to use the NMRView procedure
NvMkSpectrum. This command takes one or two arguments. The first argument is
the name of the window to be created. Thus, a window containing a spectrum widget can
be created by simply typing NvMkSpectrum noesy. If one intends to subsequently
pack additional spectrum widgets into the same toplevel window, the second argument should be
specified to indicate the packing direction. If windows are to be added horizontally,
the direction should be left or right, to pack windows against the left or right sides of
the toplevel window. If windows are to be added vertically, the direction should be
top or bottom, to pack windows against the top or bottom of the toplevel window.
A powerful alternative, is to create an array of windows automatically. In this case, the
second argument specifies the number of rows and columns of windows to be created. Thus,
NvMkSpectrum hmqc 2x4 would create a toplevel window with 2 rows, each
containing 4 spectrum widgets.
For example,
NvMkSpectrum noesy, or NvMkSpectrum noesy left will create a new toplevel window named .noesy
and will pack a spectrum widget, named .noesy.0 in it against the left side.
NvMkSpectrum cosy top will create a new toplevel window named .cosy and
pack a spectrum widget , named .cosy.0 against the top side.
The lowest command level available to the user for creating a spectrum widget is the
spectrum command which simply creates a new spectrum widget. If
the "spectrum" command is used it is the users responsibility to decide what toplevel
widget the window is to be displayed in and to explicitly use a Tk geometry manager such
as the "pack" command to cause it to be displayed. To create a toplevel window with
three spectra in it from left to right, the following commands would be used.
frame .noesy
pack .noesy
spectrum .noesy.0
spectrum .noesy.1
spectrum .noesy.2
pack .noesy.0 noesy.1 noesy.2 -side left.
While this latter method is the most complicated, it also is the most flexible.
Spectrum widgets can be packed into toplevel windows along with all sorts of
other widgets such as buttons, lists, menus, text or canvases, to create very
powerful interfaces.
Most parameters effecting the display mode of spectra are
specified in the spectral attributes panel. Spectra may
be displayed as 1D vectors or as 2D slices. The 1D
vectors can be displayed in a horizontal orientation
(1Dx) or a vertical orientation (1Dy). These display
modes (1Dx, 1Dy, and 2D) are selected with the pull down
choice in the spectral attributes window. Also, in 2D contour
plot mode you can display a 1D vector slice superimposed on the
contour plot (seed 2D mode below).
In mode 1Dx,
the two x values specify the plot limits of the vector.
The y, z and z2 values specify the particular vector in
the 2,3 or 4D matrix. If a range of values is specified
for y, z or z2, all the vectors between those values will
be drawn. In mode 1Dy, the two y values specify the plot
limits of the vector. The x, z and z2 values specify the
particular vector in the 2,3 or 4D matrix. In the 1D
modes the value specified in the Scale entry, specifies
the intensity difference between the maximum and minimum
axes. The value specified in the Zero entry, specifies
the point (as a fraction from zero to one, at which a
value with intensity zero will be displayed. For
example, in mode 1Dx, with Scale set to 100 , and Zero
set to 0.5, the the y-axis range is from -50 to +50. With
Scale set to 100, and Zero set to 0.0, the y-axis range
is from 0 to 100.
In 2D mode the spectra are displayed as contour plots.
The panel entry, Level, specifies the intensity of the
lowest contour that will be drawn. The panel entry,
LvlMul, specifies the ratio of intensities of subsequent
contours. The panel entry, #Lvls, specifies the maximum
number of contours to display. The x values specify the
plot limits along the x-axis. The y values specify the
plot limits along the y-axis.
In 2D mode "real-time" slices can be displayed that track the position
of crosshair cursor 1 (the black crosshair).
Slices can be in the x, y, z or (z2 NOT YET) dimension of the
spectrum. X and Z slices are drawn parallel to the X axis of the window.
Y and Z2 slices are drawn parallel to the Y axis of the window. The slice is continuously updated as the cursor is moved.
For 3 and 4D spectra the
specific planes to be drawn are specified with the z and
z2 (for 4D spectra) values. If a range of values for z
and/or z2 are specified, all planes between the two
specified values (inclusive) are drawn. The file
dimensions and the display dimensions can correspond in
any desired manner. The pull down choice box following
the x and ydisplay entries is used to specify which
dataset dimension is specified on the particular axis.
A few seconds after a contour plot is initiated
a Cancel button will appear in the upper left hand corner of
the plot. Click on this button to interrupt the plot in progress.
The plotting should stop shortly.
The cursor in the spectral display window can server a variety
of functions. The default function is to move the
crosshairs. Each spectral window may have two crosshairs.
Clicking the LEFT mouse button in a spectral window
displays crosshair 1, which is generally colored black.
Clicking the MIDDLE mouse button in a spectral window
displays crosshair 2, which is generally colored red. Crosshair
1 may be moved by pointing the mouse cursor near the
vertical or horizontal lines of the crosshair, pressing
the LEFT mouse button and dragging the cursor to the
desired position. The vertical and horizontal lines of
the crosshair may be moved independently. The crosshair lines
only move if the mouse button is depressed when the mouse
cursor is within about 1/2 inch of the crosshair line. To move
both lines of the crosshair press the mouse button down when
the cursor is near the intersection of the two lines.
Crosshair 2 is moved in an analogous fashion by pressing the
MIDDLE mouse button and dragging the cursor. As the
crosshairs move, the current position of both crosshairs is
displayed in ppm at the top of the window.
The difference between the two
cursor positions in Hz is also displayed.
Alternative functions for the cursor involve
interactive peak editing
and can be selected by selecting
the cursor pull-right menu in the
Spectrum Window Pop-Up Menu.
The crosshair in different windows automatically track each
other in what is generally an appropriate manner. No
commands are required to start correlated crosshair
tracking. Crosshair correlation is dependent on the label
given to each axis of the spectrum during the referencing
process. For example, consider the case where 5 windows
are open, with axis labels as indicated below.
Window-Name X-axis-Label Y-axis-Label
a 15N 1HN
b 13C 15N
c 1H1 1H2
d 1HN 13C
e 15N 1HN
If a vertical crosshair moves in window "a", the
horizontal crosshair of window "b" and the vertical
crosshair of window "e" will move. If the horizontal
crosshair of window "a moves, the vertical crosshair of
window "d" and the horizontal crosshair of window "e"
will move. The crosshair in each window only tracks the
motion of the moved crosshair if the plot limits of the
window overlap the position of the moved crosshair. Crosshair
tracking can be disabled in a window by changing the
window's axis label(s).
You can quickly navigate around spectra and peak-lists using keys on the auxiliary keypads of the keyboard.
To use this feature the cursor must be in the active window.
- Numeric Keypad
- Use the numeric keypad to zoom and pan the spectrum as follows.
- 1
- Pan down and to the left.
- 2
- Pan down.
- 3
- Pan down and to the right.
- 4
- Pan left.
- 5
- Shift view to center on crosshair position.
- 6
- Pan right.
- 7
- Pan up and to the left.
- 8
- Pan up
- 9
- Pan up and to the right.
- -
- Zoom out.
- +
- Zoom in.
- Cursor Keys
- Use the cursor keys to move up or down planes in 3D and 4D spectra, or increment or decrement
rows and columns in 1D displays of 2D,3D or 4D spectra.
- Down Arrow
- 1Dx: Move up a row.
3D,4D Spectrum: Move Down a plane.
- Up Arrow
- 1Dx: Move down a row.
3D,4D Spectrum: Move Up a plane.
- Left Arrow
- 1Dy: Move left a column.
4D Spectrum: Move Down a Z2 plane.
- Right Arrow
- 1Dy: Move right a column.
4D Spectrum: Move Up a Z2 plane.
- Paging Keys
- Use the Insert,Delete,Home,End,PageUp and PageDown keys to navigate peaklists.
Currently not functional in 3.0.
- Insert
- Undelete the current peak.
- Delete
- Delete the current peak.
- Home
- Move to the first peak of current list.
- End
- Move to the last peak of current list.
- PageUp
- Move to the previous peak of current list.
- PageDown
- Move to the next peak of current list.
This panel provides controls to specify how the spectrum will
be displayed in the window. The window header will indicate the
name of the window whose attributes are being set, and
the name of the dataset currently assigned to the window.
This panel is selected by choosing the Attributes entry of
the Spectral Display Menu.
Across the top of the panel is a menu bar that provides access to
a variety of options to control the spectral display.
- File
- This menu provides control of the dataset displayed in the window, and draw and
close options.
- Dataset
- This command brings up a
panel
displaying a
list of currently opened files. Click
SELECT to highlight the desired dataset. Then click
SELECT on the "Select" button to assign this file to the
spectral display window. This can also be accomplished
by double-clicking SELECT on the desired filename. Click
SELECT on the "Cancel" button to close file selection
window.
- Close
- Select this command to close the "Spectral
Attributes" window.
- Colors
- Select colors for positive and negative contours.
- Positive
- Use this entry to pull down a list,
"None, Black, White, Red ..." to specify what color to
use when drawing positive contour levels. If "none" is
selected positive contour levels will not be drawn.
- Negative
- Use this entry to pull down a list,,
"None, Black, White, Red ..." to specify what color to
use when drawing negative contour levels. If "none" is
selected negative contour levels will not be drawn
- Dimensions
- This menu provides control of whether the spectral display is
a one dimensional vector drawing, or a two dimensional contour plot.
- 1Dx
- In this mode the the spectrum is displayed as one or more one-dimensional vectors in a horizontal orientation.
- 1Dy
- In this mode the the spectrum is displayed as one or more one-dimensional vectors in a vertical orientation.
- 2D
- In this mode the the spectrum is displayed as a two-dimensional plot.
- Mode
- The selected entry in this menu determines whether or not contour data is
read from the matrix or a contour file..
- Live
- Data for the contour plot is obtained from the matrix file.
- Record
- Data for the contour plot is obtained from the matrix file, but the contours are
recorded in a file for future playback. Only those planes that are actually
drawn while in this mode are recorded.
- Play
- Data for the contour plot is obtained from the contour file that was created in
record mode.
- Misc.
- Various items are controlled from this menu.
- AutoClear
- If this item is active
(the default), the spectral display window will be
cleared prior to the display of the contour plot. If
inactive, the next contour plot will overlay the current
plot.
- AutoLvl
- Select this entry to automatically estimate
a contour level appropriate to the dataset assigned to
this window.
- Draw
-
Click on this button to draw the spectrum.
The next region of the panel provides three text boxes to specify the
contour level, the ratio between subsequent contours, and the number of
contour levels to draw.
- Lvl
- Type an entry in this box to specify the level at which contours are
to be drawn. This value is multiplied by a global scale parameter (set in the Prefs dialog, default 1e6) to generate the actual
value that is used. The up and down arrows provide a convenient means to
increment or decrement the contour level. Clicking on the up arrow raises the
contour level to a value equal to the current level times the current value of
the multiplier (the value in the next field).
Clicking on the down arrow lowers the
contour level to a value equal to the current level divided by the current value of
the multiplier (the value in the next field).
- Mul
- Select a value using the slider to specify the ratio between subsequent
contour levels. For example, a value of 1.5 means that each contour will
be 1.5 times as high as the previous one.
- NLvl
- Select a value using the slider to specify the maximum number of contours to
be drawn.
- Scale
- Type an entry in this box to specify the scale value at which
1D slices are to be drawn. This value is multiplied by a global scale
parameter (set in the Prefs dialog, default 1e6) to generate the actual
value that is used. The up and down arrows provide a convenient means to
increment or decrement the scale level. Clicking on the up arrow raises the
scale level to a value equal to the current level times the current value of
the multiplier (the value in the next field).
Clicking on the down arrow lowers the
scale level to a value equal to the current level divided by the current value of
the multiplier (the value in the next field).
Whenever the Level value is changed the Scale value is
changed to be 10.0 times the Level value as this generally provides
good results.
- Xoff
- Select a value using the slider to specify the offset position(from 0.0 to 1.0) at which X (and Z) slices are drawn.
be drawn.
- Yoff
- Select a value using the slider to specify the offset position(from 0.0 to 1.0) at which Y (and Z2) slices are drawn.
be drawn.
The next section of the panel controls the plot limits.
- X
-
Press the Left Mouse button over the X to pop-up a menu of predefined plot limits, or
enter values in the next two text fields to set the plot
limits (in ppm) for the x (horizontal) axis. If the entry
is followed (without an intervening space) by a "p", then
the value is considered to be in units of points of the
dataset. The minimum and maximum plot limits can be
entered in either order. These values are automatically
set to give the full spectrum when a new dataset is
assigned to this window.
The text in the third field is used as a label for the x (horizontal)
axis. This value is used to label the axis on hard copy
plots, is used for determining the correlation of cursors
between different windows (see cursors, below), and is
used during peak-picking and peak display (see Peak
Picking, below). This is automatically set to the value
assigned to the corresponding dimension (see below)
during the referencing of the matrix, but can be changed
by entering a new value in this field. 1(2,3,4) Hold down MENU over
this item to select the dimension of the matrix to be
displayed on x axis.
- Y
- Press the Left Mouse button over the Y to pop-up a menu of predefined plot limits,
or enter values in the next two text fields to set the plot
limits (in ppm) for the y (horizontal) axis. If the entry
is followed (without an intervening space) by a "p", then
the value is considered to be in units of points of the
dataset. The minimum and maximum plot limits can be
entered in either order. These values are automatically
set to give the full spectrum when a new dataset is
assigned to this window.
The text in the third field is used as a label for the y (vertical)
axis.
This value is
used to label the axis on hard copy plots, is used for
determining the correlation of cursors between different
windows (see cursors, below), and is used during
peak-picking and peak display (see Peak Picking, below).
This is automatically set to the value assigned to the
corresponding dimension (see below) during the
referencing of the matrix. 1(2,3,4) Hold down MENU over
this item to select the dimension of the matrix to be
displayed on y axis.
- Z
- Press the Left Mouse button over the Z to pop-up a menu of predefined plot limits,
or enter values in the next two text fields to set the plot
limits (in ppm) for the z (3rd Dimension) axis. If the
entry is followed (without an intervening space) by a
"p", then the value is considered to be in units of
points of the dataset. The minimum and maximum plot
limits can be entered in either order. These values are
automatically set to display the full range of planes when a new
dataset is assigned to this window. If the return key is pressed in
the first Z field, then the second field will be set to the same value.
The popup menu has a convenient entry to
select the first or last plane. The spectral display
window will be cleared prior to drawing the first plane
(if AUTOCLEAR) is set. Subsequent planes will be
overlaid on top of the first plane. To draw a single
plane, set both values equal to each other.
- Z2
- Press the Left Mouse button over the Z2 to pop-up a menu of predefined plot limits,
or enter values in the next two text fields to set the plot
limits (in ppm) for the z2 (4th Dimension) axis. If the
entry is followed (without an intervening space) by a
"p", then the value is considered to be in units of
points of the dataset. The minimum and maximum plot
limits can be entered in either order. These values are
automatically set to display the full range of planes when a new
dataset is assigned to this window. If the return key is pressed in
the first Z2 field, then the second field will be set to the same value.
The popup menu has a convenient entry to
select the first or last plane. The spectral display
window will be cleared prior to drawing the first plane
(if AUTOCLEAR) is set. Subsequent planes will be
overlaid on top of the first plane. To draw a single
plane, set both values equal to each other.
- ZoomBox
- The zoombox in the lower right corner of the spectrum provides a
graphical view of the current display region. The display region can also
be changed by interactively dragging the zoombox around. The current display
region is shown as the blue box. The position of the view can be adjusted
by pointing the cursor near the middle of the box, holding the left mouse button
down, and dragging the blue view box around. The size of the view region can be
adjusted by pointing the cursor near an edge of the box, holding the middle mouse
button down, and dragging the side to its desired position.
Before drawing a spectrum you must associate a particular dataset with
the spectral window. To do this choose "Dataset" from the "Files" menu of
the Spectral Attributes Panel. This brings up the following panel.
Alternatively, you can use the
win -dataset command.
The panel lists all datasets that have been opened.
- OK
- Associate the selected dataset with the spectral window. The panel
is then closed.
- Cancel
- Close this panel without specifying a dataset for the spectral window..
Hold down MENU (the right mouse button) within a spectral display window to
display this menu.
- Attributes
- This command will open up the spectral attributes window.
If the window is already open it will set it to display
the attributes for the active spectral window.
- View
-
The commands in this menu allow the user to change the
region of the spectrum that is displayed in this window.
- Draw
- Draw the current view.
- Expand
- This command changes the plot limits to include the region
bounded by the two crosshairs and redraws the spectrum.
- Previous
- This command
changes the plot limits to that which was active prior to the
last expansion and redraws the spectrum. The previous 8 views are saved so the
user can return to them with this command.
- Full
- This command changes the plot limits to that of full spectral
width for each of the two displayed dimensions and redraws the
spectrum.
- Center
- Center the current view on the crosshair cursor (number 1).
- Swap
- This command exchanges the view limits for the two
displayed dimensions and redraws the spectrum. The result is to
display the view
across the diagonal from the current view. This command
is only appropriate for 2D homonuclear spectra
- Edit
- This menu provides commands to copy display attributes
from one window to another.
- Copy
- This command saves the display attributes of the current
window into the copy buffer.
- Paste
- This command sets the display attributes of the current
window to those in the copy buffer.
- Cursor
- This menu can be used to switch between different cursor modes.
The use of the crosshair cursors is described in the section on
Cursors.
The use of the PeakAdjust, PeakAdd and PeakDelete modes is described in the
section on Interactive Peak Editing.
- Crosshairs
- This is the default. Moving the cursors moves crosshairs.
- PeakAdjust
- The cursor can be used to adjust the position of peak boxes.
- PeakAdd
- The cursor can be used to interactively add peaks at the
cursor position.
- PeakDelete
- The cursor can be used to interactively delete peaks at
the cursor position.
- Slice
- Use this menu to turn on "real time" 1D slices overlayed on
the 2D contour plot. Any and all slices may be on simultaneously.
- Xslice
- Display a slice through the dataset dimension displayed specified
for the X axis of the spectral display.
- Yslice
- Display a slice through the dataset dimension displayed specified
for the Y axis of the spectral display.
- Zslice
- Display a slice through the dataset dimension displayed specified
for the Z axis of the spectral display.
- Z2slice
- Display a slice through the dataset dimension displayed specified
for the Z2 axis of the spectral display.
- Peak
- This menu provides commands that allow the user to pick
and display peaks.
- PeakPick
- This command opens up a control window for peakpicking.
- Search
- This command searches through all the displayed planes of a 3D spectrum
to find the planes that contain signals above the contour level.
- Showpeaks
- This command displays (in the current window) boxes and
labels at the positions of each of the peaks in the
active peak list.
- Attributes
- This command opens up a attribute panel that controls peak display.
- Misc
- This menu provides commands control plotting and grid
display.
- Plot
- Select this entry to display a
plotting dialog
with controls for
making plot files of the active window.
- Grid
- This command causes a grid of points to be displayed on
the active window. The position of each point
corresponds to the location of an actual data point in
the dataset displayed in the window. The grid will be
drawn each time the window is redisplayed. Selecting
this command a second time will turn off the grid
display. This is very slow if the plot region is large.
It is based for small areas to observe the digitization around
a one or a few peaks.
- Unify
- This command is only active if more than one spectral window is present
in a single toplevel window. If this is the case then selecting it will
cause all the windows within the single toplevel to be drawn with the
same plot limits and contour level as that of the active window.
To plot spectra select the Misc->Plot entry from the Spectrum display window puop-up menu. The following plotting dialog will appear.
- Labels
- Use these entries to specify the labels that will be drawn on the plot.
- xLabel
- The label that will be drawn on the x axis of the plot. By default the
label for the x axis of the spectrum is used.
- yLabel
- The label that will be drawn on the y axis of the plot. By default the
label for the y axis of the spectrum is used.
- title
- The label that will be drawn on the title of the plot. By default the
name of the dataset that is assigned to the spectal window is used.
- Plot Positions
- Use these entries to specify the position of the spectral plot on the
paper. At present, the units are in inches.
- XPos
- The position of the left edge of the plot relative to the
left edge of the paper.
- YPos
- The position of the lower edge of the plot relative to the
lower edge of the paper.
- Width
- The width of the plot.
- Height
- The height of the plot.
- Output Device
- Use these entries to control the format and file for the plot output.
- Postscript
- Select this button to specify that the plot output should be Postscript.
- HPGL
- Select this button to specify that the plot output should be HPGL.
Note that this output is probably not suitable for sending to an actual
plotter. The contour algorithm used in NMRView is optimized for speed not
for keeping the pen on the page. This format can be used for importing the
output file into some software programs.
- Plotfile
- Specifiy the name of the file that the output will be written to.
- Autoprint
- Check this button to automatically send the file to the default
printer. Only works with UNIX systems that use the lpr command
for printing.
- Command Buttons
- Plot
- Plot the active spectrum.
- PlotAll
- Plot all the spectral windows contained in the toplevel
window that contains the active spectrum. The spectra will appear
on a single page in the relative positions they occupy in the toplevel
window.
- Close
- Close the plot window.
Regardless of the method used to create spectrum widgets, each such widget will be
listed in the Spectrum Manager. You can use this GUI to delete existing windows and
bring them to the front with the controls in this panel.
- Close
- Dismiss this panel.
- Delete
- Delete the spectral window that is selected in the window list above.
- To Front
- Bring the spectral window that is selected to the front of the display.
Last revised 29 Feb 1996