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User Preferences

To set and changes your preferences, choose iNMR > Preferences (on the Mac) or Help > Preferences (on Windows). The meaning of each option is explained in the table below.

To invert one or more options for a few minutes only, on the Mac hold down the alt key and choose iNMR > Timer; on Windows, choose the command Help > Timer. At the top of this alternative dialog, you find a slider to set the duration of the temporary options. After the specified duration, when the old options are restored, you'll hear an acoustic signal.

 

  ■ Miscellaneous Preferences (Processing, Navigation, Console)

Default Spectrometer Frequency

This is the value used for simulations or when iNMR can't import the frequency of a spectrum. In all cases, the user can change this value inside the individual documents.

Zero Filling Factor

When you process a spectrum for the first time, iNMR creates default processing parameters for it. In the case of mono-dimensional proton spectra, you can decide to apply zero-filling by default. This parameter answers to the question: “How many times should your 1-H spectra be filled ?” and can be a decimal number. 1 means no zero-filling. 2 means that the size of the spectrum will be doubled by zero-filling. You can change the FT size for individual spectra. Hetero-nuclear spectra must be zero-filled manually, because in most cases this is not necessary. The indirect dimension of multidimensional spectra is zero-filled by default, but it's not affected by this value.

Use Linear Prediction Filling

If this option is on, when processing an indirect dimension, iNMR implements Fast Linear Prediction instead of zero-filling. This option can be overridden, for individual spectra, inside the FT dialog.

Arrows Can Zoom

When, scrolling through the spectrum, you reach the limit of the spectral width, if you try scrolling further iNMR will expand the final part of the spectrum.

Mighty Mouse Can Scroll

Enables horizontal scrolling with the mighty mouse scroll ball. If disabled, the scroll ball only changes the amplification factor.

folder containing your scripts

To access your custom Lua scripts, you should store them into a folder whose path is declared here. The folder can be organized into sub-folders. Press the button “choose” to set or change the folder via the standard Choose Folder dialog. If, instead, you write the absolute path, don't use the tilde character.

shortcut buttons

You can create shortcuts to your favorite scripts that will appear like buttons inside the iNMR console. The scripts must reside at the top level of your scripts folder and their names should not contain spaces. To create the buttons, insert the names, without extension, into this field, separated by spaces.

 

  ■ Display Preferences

Colors

You can define the 6 colors used by iNMR to draw:

  1. 1-D spectra and positive contour levels.
  2. Integrals curves and negative contours.
  3. Marks and scale labels on the screen (not when printing).
  4. Peak-picking digits and lines.
  5. The background.
  6. The scales (including their labels when printing) and the integral regions with their labels.

Changing the first two colors inside the preferences dialog has no effect on existing documents, because they already have their own individual colors; they can be changed with the command Format > Levels & Colors. The colors from 3 to 6 are shared by all the documents.
The six default colors have been chosen for a reason: they are a good combination, in practice. Many routines have been designed having these default colors in mind. Remember it!

Fast Plot

All the 2-D spectra drawn in the fast plot mode share the same palette of colors. You can choose it here from a list of 8 palettes or, better, use the keyboard shortcuts 4 and 6.

1D margins (left & right)

Initial space, in screen units, between the edge of the plot and the edge of the window, when a new document is created.

2D margins (top & bottom)

Like above, but for the top and bottom margins.

Gap under the Projections

This parameter inserts a gap between a 2-D plot and the projections displayed along the edges.

Integral Curves Offset

Initial distance, in screen units, between the base level of the spectrum and the base level of the integral curves, when a new document is created..

Short Distance (in screen units)

  • The initial distance between the 1-D spectrum and the frequency scale (or the integrals brackets, if present).
  • The minimum height for a peak to be picked, when no other hint is given.
  • The size of the small tick drawn over the picked peaks.

Page Size

New documents are created with the Free Size mode disabled.
If you print your spectra very often, activate this option and your new documents will be created ready to be printed (you can skip the Page Setup dialog). The proportions of the window will be the same as those of the paper used.
The Free Size, instead, is ideal for studying the spectra directly on the screen.

Retina Display

iNMR normally draws lines that are wide 1 logical point. With a Retina display 1 point corresponds to 2 pixels and lines so large are drawn very very slowly. This option tells iNMR to make the lines 0.5 points wide. In practice you are forced to use this option if you have a Retina display.

Doc Notes Preferred

If ON, new notes are Document Notes (defined in window coordinates). If OFF, new notes are Peak Labels (defined in frequency coordinates).

Dashed Negative Contours

Useful, when you have a B&W printer, to differentiate between positive and negative contour levels.

 

  ■ Output Preferences

Print Frame

Prints a black frame around the spectrum.

Print File Name

Prints the window title in the upper-left corner.

Print Title

Prints the internal title (usually a description of the experiment).

Show the Title Inside the Document Window

The internal title is displayed on the screen, but not printed.

Print Date

The current date is printed.

Resolution

When drawing on the screen, the individual data-points are partially collapsed, because usually there are many more data points than screen points. If this parameter is set to 1, then the data points are also collapsed when printing. This makes printing faster, but is detrimental for the quality and accuracy of the plot. You should therefore set this value to 4 at least, which means that the horizontal resolution, when printing, is four times higher than on the screen. In the unlikely case in which there are more screen points than data points, this parameter is irrelevant. When exporting a bitmap, this setting has a different meaning. It says how many times the bitmap is wider and higher than the window.

Line Thickness

The thickness of the line used to draw spectra, in screen units. Thin lines look faint on the screen, but look good when printed on paper.

 

  ■ Digits Preferences

Font and Size for Digits

The font settings for everything: scales, integrals, peak-picking, etc.. When a spectrum is created, it starts with these default values. Afterwards, each spectrum can use a different font and/or size.

Font and Size for Notes

This is an optional setting that, if defined, is used for new annotations only. When created, however, each note can have a different combination of font, size and color.

Font Panel

This button opens the Font Panel for either the Digits or the Notes, whichever is selected at the left.

Clear

Clears the Font settings for the new notes. New notes will be created with the same font and size used for digits.

digits for integrals

Default value for new documents. It can be overridden for single documents. When there are exactly three significant digits, the decimal zeroes are not shown.

digits for peak-picking

Number of significant digits. This is a global setting that is shared by all documents.

digits for marks

Marks are temporary straight lines that are not printed.

 

  ■ Files Preferences

Automatically Save Documents When Closing

iNMR will not prompt the user to save changes to a modified document when the window is closed and will save the document silently. Different is the case when you quit iNMR: the program will always ask if you want to save the changes.

Create Back-Up File

Automatically creates a back-up file with the extension .back instead of .inmr.

Do Not Save Overlays

Overlays are normally persistent, unless the corresponding files are moved. With this option, overlays are not persistent: they are forgotten as you close their hosting window.

generate Thumbnail (Mac Only)

Creates a thumbnail whenever you save a document. The thumbnail is an image of the first page and is required by the Quick Look technology introduced with Mac OS 10.5.

generate Preview (Mac Only)

Creates a preview whenever you save a document. The preview is a full PDF representation of your spectrum for the sake of the Quick Look engine. When the preview is not present, Quick Look shows a list of metadata.

Export ASCII Lists with Comma Separated Values

Lists of integrals or data points are normally tab-separated. When this option is on, the values are instead separated by a comma.

show folder names in the title bar

The name of NMR files, at least those coming from the most popular spectrometers, are often generic (e.g.: 1, 2, 3...). Unless you rename them, it's necessary to report the name of the surrounding folder, or the whole hierarchy of folders, to identify a spectrum. With this option you set the number of hierarchical folders whose names will be reported inside each window title bar. The number can go from zero up to 5.

Sidebar in new docs

You can create several display styles inside each document, that are called pages. The optional sidebar shows the miniatures of these pages. If you save a document with the sidebar visible, you will find it in the same state when you open the document again. With this option on, new documents are already created with a sidebar.

Import Processed Data When Possible

If you have already processed a Bruker spectrum on the spectrometer, the corresponding data set contains both the time domain and the frequency domain spectra. If you are not interested to reprocess the FID with iNMR, turn this option on and iNMR will read the processed spectrum instead.
Rarely a 2rr file is stored as sub-matrices. It will appear as a mess into iNMR. It is necessary to translate the file with CARA. You will be using two CARA commands: “Tools > Open Spectrum...” and “Spectrum > Export EASY Spectrum...”. When prompted “Please enter the number of submatrices” always reply 1 (no submatrix). The final EASY files must be stored outside the Bruker data set.

Show the FID when Opening a Document

When you open a spectrum with iNMR for the first time, the program will show the raw data points for your inspection. You can choose between applying the default or any special processing. If, instead, the spectrum has already been processed with iNMR in the past, the program assumes that you are already satisfied with the saved processing parameters and applies them again. You'll see the document in the same state it was when you saved it. By turning this option on, iNMR will instead wait your instructions in all cases: when you reopen a document, the program will simply reload the raw data points.