Add
To create a new spectral window choose "Add" from the Windows entry of the
Control Panel menu bar. The following panel will appear. Alternatively,
you can use the win -cre command.
- OK
- Click on OK to open a new spectral window with the name specified in
the text field of this panel. A new window will be created and the panel
closed. If the name specified is already in use by another spectral
window an error message will appear, and the window will not be created.
- Cancel
- Click on this entry to close the panel without opening a new window.
You can 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.
Hold down MENU 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.
- 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
- This command plots the current spectral window. Plots
have the same aspect ratio in the hardcopy as they do on the screen.
A
postscript file "plot.ps" is generated and sent to the
default printer.
- PlotAll
- If a window has daughter windows, this command
will plot all the daughters. The windows will have the same
layout on the hardcopy plot as they do in the screen window. A
postscript file "plot.ps" is generated and sent to the
default printer.
- 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.
- Daughter
- This command creates a new daughter window in the current active window.
See the
win -dau
command for more information.
- Mouseaction"
- This command displays a the following panel in which
mouse actions can be specified for the active window.
For more information see the
win -mouse command.
- User
- This menu is initially blank. It can be set
interactively by the user using the
win -menu command.
This panel provides controls to specify display in the
spectral windows. 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
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.
- Done
- Select this command to close the "Spectral
Attributes" window.
- Draw
- Select this command to draw the spectrum
in the spectral display 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 orienation.
- 1Dy
- In this mode the the spectrum is displayed as one or more one-dimensional vectors in a vertical orienation.
- 2D
- In this mode the the spectrum is displayed as a two-dimensional plot.
- Planes
- This menu provides commnds to move up or down planes in 3 or 4D spectra.
- Increment Z
- Move up one plane in the Z dimension.
- Decrement Z
- Move down one plane in the Z dimension.
- Increment Z2
- Move up one plane in the Z2 dimension.
- Decrement Z2
- Move down one plane in the Z2 dimension.
- 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.
- Reset
- Select this entry
to reset the displayed attributes to the windows current
values.
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.
- Level
- 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 paramter (set in the usprefs 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).
- 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
paramter (set in the usprefs 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.
- 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.
- 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
- 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 the xaxis.
- Y
- 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. 1(2,3,4) Hold down MENU over this
item to select a second dimension of the matrix to be
displayed on the y axis.
If this value is not 0, the
resulting contour plot will consist of a diagonal plane
through the spectrum. The size (in data points) of the
two dimensions applied to the single axis must be the
same for this to work. This is generally only
appropriate to homonuclear 3D spectra. THIS FEATURE IS
NOT CURRENTLY ACTIVE.
- Z
- 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 first plane when a new
dataset is assigned to this window. 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
- 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 first plane when a new
dataset is assigned to this window. 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.
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..
This panel provides controls to specify the display of peaks in the
spectral windows. 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.
The panel is displayed by selecting the Attributes option of the
Peak Menu in the Spectral Display Menu.
- Col On
- A pull-down menu of colors. If colortype is set to "plane",this specifies the color of peaks that
are within the range of displayed planes. This mode is only applicable to three or four
dimensional spectra.
If colortype is set to "assigned", this specifies the color of peaks that
have been assigned to specific atoms.
- Col Off
- A pull-down menu of colors. If colortype is set to "plane",this specifies the color of peaks that
are not within the range of displayed planes, but are no more than "offset"
number of planes outside this range. This mode is only applicable to three or four
dimensional spectra.
If colortype is set to "assigned", this specifies the color of peaks that
have not been assigned to specific atoms.
- Col Type
- Specifies how the color of peaks is determined.
- Plane
- Color is determined by whether or not peaks are within the range of displayed
planes.
- Assigned
- Color is determined by whether or not peaks have been assigned to specific
atoms.
- Error
- Color is determined by the value of the Error field for the peak. If any
dimension has a value not equal to "++" then the peak is drawn in the "Col Off"
color.
- Lab Type
- Specifies how the label displayed with each peak is determined.
- Number
- The label is the peak number.
- Label
- The label is composed of the assignment labels for each peak dimension.
- Residue
- The label is composed of the unique residue numbers from the
assignment label for each peak dimension.
- Atom
- The label is composed of the atom fields from the
assignment label for each peak dimension.
- Dis Type
- Specifies how the peak is displayed.
- Box
- The peak is drawn has a box centered on the peak position, with a width
equal to the peak bounds. A label is placed at the corner.
- Simulated
- The peak is drawn with simulated contours. The intensity and linewidth
for the simulation are taken from the peak intensity and width.
- Label
- The peak position is labelled, but a box is not drawn.
- Offset
- Peaks are displayed that are within this number of planes of the
range of planes that are displayed (for three and four dimensional
spectra). For example, if planes 17 to 18 are currently being displayed
in the spectral window, any peak that was closest to planes 17 to 18 would
displayed, with the color selected in the "Col On" menu. Any peaks closest to
planes 13 to 16 or 19 to 22 would be displayed with the color selected in
the "Col Off" menu. Peaks outside of this range of planes would not be displayed.
- Show Peaks Menu
- This menu controls the response of the spectral window to
actions taken in the peak analysis window.
- None
- If this item is selected, no action will occur in this
window in response to peak selections in the peak
analysis window.
- Expand
- If this item is selected an expansion of the spectrum
around a particular peak will appear when a peak is
selected in the Peak Analysis window. The width of the
display region around the peak will be automatically set
to five times the peak width in each of the display
dimensions.
- ExpandFixed
- If this item is selected an expansion of the spectrum
around a particular peak will appear when a peak is
selected in the Peak Analysis window. The display limits
will be changed so that they are centered on the new
peak, but the width of the display region will not change
from the current values.
- Plane
- If this item is selected the spectrum will be plotted at
the particular plane(s) corresponding to the peak
selected in the Peak Analysis window. The x and y plot limits
will not change from the current values.
- Links
- If this is selected then peaks that have "links" between them will
be drawn with a line connecting them.
- Display Peaks Menu
- This menu controls whether or not peak boxes and labels
are drawn in the spectral window when the spectrum is
redrawn. Hold down MENU to select a peak list to be
displayed in the window. Peak boxes or simulations will be drawn for any
peaks from the selected peaklist that are within the
limits of the window, whenever the contour plot is
displayed.
- Close
- Close this panel.