- Name
- Enter the name of the peaklist. If mode (see below) is "New" there must not
be an existing peaklist with this name. If mode is "Append" or "Replace", there
must be an existing peaklist with this name.
- Mode
- Specify whether to create a new list, replace an existing one or append to
an existing one.
- New
- Picked peaks will go into a new peaklist.
- Replace
- Picked peaks will replace an existing peaklist.
- Append
- Picked peaks will be appended to the end of an existing peaklist.
- Region
- Specify whether to pick the entire region of the displayed in
spectral window, or just that within the crosshair box.
- Window
- Peakpick the entire region displayed in spectral window.
- Box
- Peakpick the entire region within the crosshair box.
- Folded
- Select the boxes corresponding to any dimensions of the spectra that were
folded (collected with a sweepwidth narrower than the expected region of
peaks. The peakpicking search will then properly wrap to the other side
of the spectrum for any peaks that are on the edge of the spectrum. This ensures
that the center and with of edge peaks are properly determined, and that they are
only picked once.
- MinWidth
- Any peaks with bounds less than that specified (in data points) will be flagged in their error
field with an "N" for narrow.
These peaks will display in a red color during peak picking.
Perhaps it would be better to just automatically delete such peaks?
- MaxWidth
- Any peaks with bounds greater that that specified (in data points) will be flagged in their error
field with an "W" for wide.
These peaks will display in a red color during peak picking.
Perhaps it would be better to just automatically delete such peaks?
- Pick
- Do the peakpick.
- Close
- Close the peakpick panel.
This panel can be displayed by selecting "Peaks" from the "Analysis" menu of the control panel.
- Move
- Menu for moving through the peak list.
- First
- Move to the first peak in the active peak list.
- Previous
- Move to the previous peak in the active peak list.
- Next
- Move to the next peak in the peak list
- Last
- Move to the last peak in the peak list.
- Edit
- Menu for editing the peak list.
- List
- Display's a panel with attributes describing the
current peak list.
- Compress
- Compresses the peak list by permanently removing peaks that have
been marked for deletion. After compression, deleted peaks cannot be
restored!
- Cluster
- Display's a panel with controls for clustering peaks. NOT YET ACTIVE
- Couple
- Display's a
panel,
with controls for coupling peaks.
- ID
- Display's a panel with for identifying peaks. Particularly useful
for identifying noe peaks.
- Fit
- Extract data about the peak from the dataset and send it to the XY analysis routines for peak fitting to the model currently selected in the XY equations control. The non-linear fit is performed and the peak data updated.
- Restore
- Resets the displayed peak attributes to those present prior to typing in
the peak fields. After the return key is hit, the change's are permanent and
can't be restored with the "Restore" function.
The data display portion of the Peak Analysis window displays
data about the current peak. New values can be entered in
each field. After typing in a new value, you must hit
the Enter key to make the change. The newly entered
data will be saved immediately to the database.
The fields are as follows:
- Atom Lab
- Enter a value here to assign a peak. The entry must conform
to the format of a
peakSpecifier,
for example, 3.ca.
or must be a question mark "?" if the peak is unassigned.
Tentative assignments can be entered by preceding the peak
specifier with a question mark. For example, ?3.ca.
- Center
- The chemical shift at the center of the peak.
- Width
- The half height peak width.
- Bound
- The width of the peak at its base (the contour level active when the peak was picked).
- J
- The splitting of the peak in this dimension. This is generally, only specified
after the peak coupling action.
- LinkA
- Not yet active, this will specify a link to another peak with the same label.
- LinkB
- Not yet active, this will specify a link to another peak with the same label.
- Thread
- Not yet active, this will be a unique number for all linked peaks.
- Error
- The error code returned when the peak was picked.
Use this panel to collapse pairs of peaks that differ by less than a specified
chemical shift difference (in Herz). Typically, a value larger than the expected
coupling is specified in one dimension, and a value larger than the expected
error in peak position is specified in the second dimension. When used on
small couplings (typically less than 20 Hz) the Min value is left at 0.0 for
each dimension. In systems with large couplings, for example the 1-bond
Ha-Ca coupling in peptides the Min value for the dimension with the large
coupling can be set to a value just smaller than the smallest expected coupling. For example, 120 Hz, for a Ha-Ca coupling. Only crosspeaks that differ by at least the Min value will be collapsed to a single peak. This aids in recongnizing the appropriate pairs in complex spectra. If the "Antiphase" button is selected only pairs of peaks with opposite phase will be collapsed. This provides
additional selectivity. Two collapse 2D proton COSY spectra this coupling
process can be repeate several times, swapping the two Max values each time, to succesively collapse complex multiplets.