USING NMRVIEW
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 entery, 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 maxinum
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 desried 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.
To interrupt a contour plot in progress, place the mouse pointer in the
window from which NMRView was started, and press ctrl-C. The plotting
should stop shortly.
Each spectral window may have two crosshair cursors.
Clicking the LEFT mouse button in a spectral window
displays cursor 1, which is generally colored black.
Clicking the MIDDLE mouse button in a spectral window
displays cursor 2, which is generally colored red. Cursor
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 cursor may be moved independently. The cursor lines
only move if the mouse button is depressed when the mouse
cursor is within 1/2 inch of the cursor line. To move
both lines of the cursor press the mouse button down when
the cursor is near the intersection of the two lines.
Cursor 2 is moved in an analagous fashion by pressing the
MIDDLE mouse button and dragging the cursor.As the
cursors move, the current position of both cursors is
displayed in ppm at the top of the window. The color of
the position display is the same as the color of the
corresponding cursor. The difference between the two
cursor posiions in Hz is also displayed.
The cursors in different windows automatically track each
other in what is generally an appropriate manner. No
commands are required to start correlated cursor
tracking. Cursor 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 cursor in each window only tracks the
motion of the moved cursor if the plot limits of the
window overlap the position of the moved cursor. Cursor
tracking can be disabled in a window by changing the
window's axis label(s).
To pick peaks in a particular region of the spectrum,
display the region in any spectral window. Then choose
PeakPick from that window's pop-up menu. The PeakPick
Control Window will appear. Type the name that you wish
to be associated with the new peaklist in the text field
of the control window. Click on the Pick button to start
the automatic peakpicking. As peaks are identified in the
spectrum, boxes annotated with the peak number will be
drawn on the spectrum at the position of each identified
peak. The boxes will be drawn in either the color green
or the color red. The peaks that are boxed in red
violate some criteria. Peaks that are too narrow or are
too wide will be red. The minimum and maximum width
criteria can be set for each dimension in the PeakPick
Control Window. At present, these criteria are specified
in units of data points. Peaks that are on the edge of
the spectrum will also be colored red. Peaks that
violate any of these three criteria will be stored in the
peak list, but the error field associated with each peak
dimension will denote the violation with the symbols N,
W, or E (for narrow, wide, or edge).
Some spectra, especially 3D and 4D spectra, may be
collected with a sweep width narrower than the frequency
range of the spectral peaks. In these spectra, peaks are
folded to a position that differs from their true
position by an integer multiple of the sweep width. Peaks
on the edge of such spectra "wrap" arround to the
opposite edge. To properly pick spectra with such
wrapped peaks, check the Fold box in the PeakPick Control
Window for the desired dimension(s). When Fold is
selected the peakpicker will wrap at the edge of the
spectrum so that the peak width and position are properly
determined.
To pick peaks in a specified region of the spectral
window, place the crosshair cursors so as to box in the
desired region. Select the Box attribute in the PeakPick
Control Window. Now, only the region within the box will
be analyzed for peaks. To pick peaks in the entire window
select the Window attribute instead.The peaks that are
picked may be stored as a new peak list, they may replace
an existing peak list, or they may be appended to an
existing peak list. The desired option may be selected
from the pulldown list that specifies the New, Replace,
or Append Attributes.
Peaks in the peak lists may be displayed on spectra in a
variety of ways. The first method is to select the
Showpeaks entry from the spectral windows pop-up menu.
This will result in the display of peaks from the peak
list currently selected in the Peak Analysis Window. The
peaks will be drawn as rectangular boxes centered on the
peak position. The boxes are labelled in the upper right
corner. By default the label is the peak number, but
this can be changed to display atom and/or residue
information with the
win -peak_lab_type command. With 3D
and 4D spectra, only peaks whose z and/or z2 dimensions
are within a specified number of planes of the planes
currently displayed will appear. The range within which
planes are displayed is specified with the win -peak_off
command. Peaks whose z and/or z2 dimensions are closest
to the display plane appear with the color red. Those
peaks that are off the display planes, but within the
specified range appear with the color green. These colors
may be changed with the win -peak_col_on and win
-peak_col_off commands. Alternatively, the color choice
may be based on whether the peak has been assigned
(defined as the lack of a ? in the peak label fields).
This option may be selected with the win -peak_col_type
command.
The second method to display peaks is by selecting the
desired peak list name from the Display Peaks pull-down
list in the Spectral Attributes Window. If a peak list
is selected in this pull-down list, that peak list will
be automatically displayed whenever the window is
redrawn. It will also appear on hard-copy plots. All
peak display options operate as described in the previous
paragraph.
Finally, peaks can be displayed using the command, win
-showpeaks. This is equivalent to selecting the
Showpeaks entry in the spectral display pop-up window.
The position and size of peaks can be edited interactively using the mouse.
To change the position of a peak, point to the center of the peak with the mouse.
While holding the Left Shift Key down, press the left mouse button down. Now,
while keeping the left mouse button down you can drag the peak around the screen
to its new position. Editing the bounds of the peak is done in a similar
manner using the middle mouse button.
Point to the center of the peak. While holding the Left Shift Key down, press
the middle mouse button down. Now,
while keeping the middle mouse button down you can drag the corner of the peak
box around to its new position. Don't be alarmed when the peak shrinks to a point
when you first press the mouse button down. This is normal, simply drag the peak bounds back out to the desired size. To interactively delete a peak, point to the
center of the peak, hold the Left Shift Key down, and double click the left
mouse button.
You can quickly navigate around spectra and peak-lists using keys on the auxilliary 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.
- 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.
NMRView stores a variety of information in a database. By default this database is named "NMRView.gdbm". When NMRView starts up it will look for a file with
this name.
If it finds this file it will attempt to open it. If it doesn't exist in
the current directory it will create an empty database named "NMRView.gdbm". The database can only be opened by one person at a time. The database is
always kept current so that even if NMRView crashes all information stored
in the database should reflect the information in memory at the time of the
crash. A different database can be specified on the command line when NMRView is started.
Included in the database are the peaklists, the chemical
shift assignments, the molecular topology of any sequence currently in use,
and the coordinates of any structures that have been read into NMRView. Development is ongoing to add additional features to the database.
The best way to read a molecular structure into NMRView is to first read
a sequence file in NMRView format (the same as that used by PEGASUS).
A sequence file consists of a line for each residue, each line containing the
three-letter code for the amino-acid. NMRView will try to find a corresponding
residue in its residue library, (in the directory $NMRVIEWHOME/reslib) and read in the molecular topology. To read a sequence use the
sread -seq command.
The topology will be stored in the current database, and need not be read in again during future NMRView sessions.
To read in molecular coordinates (after having read the topology) use the
sread -xyz command to read
xyz coordinates from files in the Brookhaven Protein Data Bank (PDB) format. The file will be scanned and coordinates of atoms whose name and residue number match an atom
in the internal topolgy will be read in.
These coordinates will also be stored in the current database, and need not be read in again during future NMRView sessions.
Up to 100 structures can be read and stored in separate memory locations.