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Getting Started with wxNUTS

Getting Started

The program now has the ability to open up to 4 files simultaneously, and to swap which file is displayed. This feature was created to allow 2D contour plots to be overlaid, but it also allows each to be viewed independently. See description of 2D Overlay for details.

Commands are not executed until <ENTER> is typed. Commands are not case-sensitive. As characters are typed, they are displayed on the gray status bar at the bottom of the window. Some commands allow arguments to set options related to execution of the command. Where applicable, menu items list the corresponding keyboard command. Helpful hints are displayed on the status bar when the mouse is rested on items in the menus.

The vertical scale of the spectrum is adjusted with the up/down arrow keys, or the < and > keys, or with the mouse wheel. Larger changes can be made with Page UP and Page Down keys. The cursor can be used to display peak frequency information.

Files in NUTS format can be opened with GA. This includes the current (type 3) data format and also previous NUTS formats (type 1 and 2). Files in their native spectrometer format must be opened with IM. Both commands are available from the File menu. Currently, the supported formats are JEOL Delta; Varian; QE; GE Medical Systems; and Bruker X-Win, TopSpin, and Aspect 3000 files.

Note to Mac OSX users: When importing data consisting of a folder containing multiple files, the Mac OS sometimes converts the folder to a “package”, which MacNUTS cannot open. The folder will have a name such as “mydata.fid”. Rename the folder to remove the file extension (eg, so it is just “mydata”). The Mac OS will then recognize it as a folder, and allow you to open it and select the files within it.

A series of commands can be executed using macros.

Preferences – customized settings are saved in a text file called wxNUTS.ini.

The program is structured with a “base” level and subroutines. Subroutines include:

Fix Baseline and segmental baseline correction – interactive polynomial baseline correction (requires 1D or Full version)
Define Peaks – peak picking
Line Fitting – fit a series of Lorentzian/Gaussian peaks to the experimental spectrum (requires 1D or Full version)
Notes – add text annotations to the spectrum
Phase – phasing with the mouse
View – to view slices of arrayed or 2D data; use Right and Left arrow keys to step through slices
Stacked Plot of 2D data
Inset plots
Zoom – expand the spectrum; also, set chemical shift reference
Buffers – display multiple 1D spectra for comparison (requires 1D or Full version)
Spectrum simulation from shifts and coupling constants
Relaxation and kinetics analysis
Resolution enhancement
Viewing GE in vivo spectroscopy data

While in subroutines, commands are single-letter commands executed immediately, not requiring <ENTER> to be executed. The name of the subroutine is printed on the gray status bar at the bottom of the window. Type <ENTER> to exit the subroutine and return to the base level.

Intensity and Contour Plots of 2D data are not subroutines, but rather an alternate display mode. 2-letter commands, with <ENTER> are still active, as in the Base (1D) level. The command to exit the 2D mode, and return to 1D, is 1D (rather than <ENTER>, as is done with subroutines). See also 2D Overlay to display multiple contour plots simultaneously.

A Data Table can be displayed on the screen, into which spectral data such as chemical shifts, splittings and assignments, can be entered.

A Command Log has been added, which logs commands executed during processing. The command log is saved in the file header. This is a work in progress, not all parameters are currently captured. The command CmdLog copies the current command log into the clipboard, from which it can be pasted into any text editor for viewing.

For 2D data (or arrays of 1D data), it is important to keep in mind whether a command will be applied only to the currently displayed slice, or to all slices in the data. Many commands, by default, act on all slices. This includes apodization functions, FT and manual phasing. Conversely, auto-phase (AP, QP and QA) is applied to only to the currently displayed slice. Several commands accept an argument, “this“, to indicate that the command should be applied only to the currently displayed slice. Commands having this option are:

FT (also other transforms, HT, IT)
LS and RS
MC and M2

2D data must be processed differently depending on how it was acquired (magnitude, hypercomplex, tppi, states-tppi or echo-antiecho). See description.

See command list.

Differences from NUTS

Last updated: 3/16/10