This popup allows the user to edit various details and parameters of the spectra within the current project.

Spectra

The Spectra tab provides a table with general information about the spectra in the Analysis project:

The Experiments: Edit Spectra popup (Spectra)

Spectra table

Contains general information about the spectra in the project.

#

The spectrum number.

Experiment

The name of the experiment used to generate the spectrum data.

Spectrum

The name of the spectrum.

Dims

Number of dimensions of the spectrum.

Active Peaklist

The currently active peaklist. The active peaklist is the list to which new picked peaks are added, from which peaks can be selected, deleted etcetera. 

Num Peak Lists

The total number of peaklists defined for this spectrum.

Scale

The relative intensity scale of a spectrum. This option affects the contours of the spectrum and thus the peak picking parameters. 

Noise Level

The estimated noise level of the spectrum.

Data Type

Shows the data type of the spectrum, e.g. raw data or processed data.

Simulated?

Indicates whether it is a simulated spectrum or not.

Data Path

The location  of the spectrum data file. 

Display Options

This Tab allows the user to view and edit the settings for the appearance of spectra in the project.

The Experiments: Edit Spectra popup (Display Options)

Display Options table

Lists the display options for the spectra in project.

#

The spectrum number.

Spectrum

The name of the spectrum.

Positive colors

Sets the colors for positive contour levels.

Negative colors

Sets the colors for negative contour levels.

Slice Color

Sets the color of the 1D slices, if displayed.

Box Visible?

Sets whether to display the box showing the fundamental region of the spectrum in the X and Y axes.

Shortcut

The number key shortcut for toggling the display of a spectrum on and off.

Rank

Sets the priority order for spectra (contours) in spectrum windows displays.

Positive Contours

Shows the positive contour levels. Double clicking opens the Edit spectrum contour levels popup.

Negative Contours

Shows the negative contour levels. Double clicking opens the Edit spectrum contour levels popup.

Try Precalc Contours

Used to toggle the use of precalculated contours. Precalculated contours speed up the display of spectra, but contour levels cannot be changed in the spectrum windows. Precalculated contours are stored in so called Contour Files that can be created using the [Contour Files] button (see below). 

Peak Font

Sets the font of the peaks for this spectrum.

Peak Pointer?

Sets whether to use pointer from the peak to its annotation.

Contour Levels

Opens the Edit spectrum contour levels popup to set the contour levels.

Contour Files

Opens the Edit spectrum contour files popup to create and modify the contour files.

Set Ranks From Order

Sets the spectrum ranks based on the order of the spectra in the table.

Referencing

This Tab allows the user to view and edit the settings for the referencing of spectra in the project.

The Experiments: Edit Spectra popup (Referencing)

Spectrum

The name of the spectrum.

Use reduced dimensionality options

Toggle to hide / show reduced dimensionality option.

Reference changes keep constant peak

Sets the parameter that is to be kept constant when changing the reference of a spectrum in this popup. Options are to keep either the point or the ppm value of the selected peak constant. Keeping the point constant means that with a referencing change the peaks move with the contours on the screen. Keeping the ppm constant means that the peaks stay where they are on the screen.

Referencing table

This table lists all the information relevant for the referencing of a spectrum for all its dimensions. The shown options are dependent on whether reduced dimensionality options are switched on or off. 

Dim

The dimension number.

Sub Dim Name

The sub dimension name. This is a reduced dimensionality option.

Isotope

The observed isotope for the dimension.

Scaling Factors

....... This is a reduced dimensionality option.

Spectrometer frequency (MHz)

The spectrometer frequency in the given dimension in MHz.

Spectral width (ppm)

The spectral width in ppm.

Spectral width (Hz)

The spectral width in Hz.

Reference ppm

The reference shift in ppm in the given dimension.

Reference point

The reference point in the given dimension.

Orig. number of points

The original number of points (e.g. after Fourier transform and before range reduction).

Point offset

The point offset (relative to the original spectrum, e.g. after Fourier transform).

Minimum aliased frequency (ppm)

The minimum aliased frequency in the given dimension. If not set this is taken to be the minimum ppm value of the fundamental region in the given dimension.

Maximum aliased frequency (ppm)

The maximum aliased frequency in the given dimension. If not set this is taken to be the maximum ppm value of the fundamental region in the given dimension.

Add Sub-dimension

Adds a sub-dimension.

Remove Sub-dimension

Removes the selected dubdimension.

Tolerances

This Tab allows the user to view and edit the settings for the tolerances of spectra in the project.

The Experiments: Edit Spectra popup (Tolerances)

Spectrum

Allows selection of a spectrum for which tolerances are displayed.

Tolerances table

Edit documentation here.

Dimension

The dimension number.

Isotope

The observed isotope for the dimension.

Assignment Tolerance

The tolerance used when assigning peaks in this dimension of the selected spectrum. This tolerance is used to specify the maximum difference in chemical shift between a peak and the shifts of the resonances it could possibly be linked to.

Shift Weighting

Specifies the relative contribution that a spectrum dimension makes to the calculation of chemical shift for a resonance. A resonance's chemical shift is calculated by considering the position of all of the peaks to which it is connected. However, by setting this weighting the user can specify that not all spectrum dimensions contribute equally to the derivation of chemical shift. For example the user may want spectra with more precisely defined peak positions to have a greater influence on the chemical shift values.

This value defaults to 1.0 for all spectrum dimensions. Setting the value adjusts the contribution of the dimension proportionately. For example setting to 0.5 and leaving other spectra at 1.0 means the other spectra have twice as much weight when calculating the shift from peak positions.

Tolerances table 2

This table shows an overview of all the tolerances settings for all the spectra.

#

The spectrum number.

Spectrum

The name of the spectrum.

Dim Assign Tolerances

Overview of all the assignment tolerances in the different dimensions.

Dim Shift Weights

Overview of all the chemical shift weights in the different dimensions.

Propagate Assignment Tolerances

Propagates the assignment tolerances from one spectrum to others. 

Propagate Weights

Propagates the chemical shift weights from one spectrum to others.

File Details

This tab allows the user to edit various file details of the spectra within the current project.

The Experiments: Edit Spectra popup (File Details).

Spectrum

Allows selection of a spectrum for which tolerances are displayed.

Data File Details

Edit documentation here.

File name

The full data file name of the spectrum.

Is data big endian?

Whether the data is big endian (e.g. originated on Bruker, SGI, Sun) or little endian (e.g. originated on Windows, Linux).

Bytes per word

The number of bytes per word of data, almost always 4.

Data number type

Whether the data is stored as integer or floating point numbers.

File header size

The file header size. For Azara data this is usually 0, for Felix data this is 16384, for NmrPipe data this is 2048 and for UCSF data this is 180 + number of dimensions *128.

Choose File

Allows the user to select a file through the Browse files popup.

Update Details

Updates the spectrum file details with the chosen values after confirmation through the Update file details popup.

File Details table

This is the table that lists some of the file details.

Dimension

The dimension number.

Number Points

The number of points for the spectrum in the given dimension.

Block Size

The block size for the data file in the given dimension.

Data Locations

This tab allows the user to edit data locations of the spectra within the current project.

The Experiments: Edit Spectra popup (File Details).

Data Locations table

This table lists all the information on the data locations of the spectra in the project.

#

The spectrum number.

Absolute Path

The absolute file path on disk of the data file.

Relative Path and File

The relative file path on disk of the data file.

Spectrum / Image

The spectrum or image name.