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.