Exporting the Spectrum
In its standard form, this command is the perfect equivalent to the command “Save As...” found in other programs. The practice of saving processed data in NMR is often the cause of the loss of the original (and more important) time domain data. While processed data can be easily, swiftly and automatically recreated starting from the FID, the opposite is normally impossible, or problematic at the very least.
If you know what you are doing, use this command, but always keep your original data. Normal users will never need the Export command. This is the reason why it is not called “Save As...”.
Exporting a Submatrix
When the spectrum has 2 or 3 dimensions and is at least partially transformed, you have the option of saving only a portion of it. In 3D spectroscopy, for example, the relevant portion of the spectrum can amount to as little as the 10% of the whole. Working with a smaller file, iNMR can go much faster.
You can also export a spectrum in ASCII format. A bidimensional spectrum is saved in form of a table: the first column contains the frequencies, in ppm units, while all other columns corresponds to rows of the spectrum.
In the 1D case you can also create a table with 2 columns (frequency - intensity). This option is labeled “ASCII x+y”. Alternatively you only export the intensities (the corresponding menu item is: “ASCII intensities”). iNMR is able to reimport the frequency-domain spectra it has exported in ASCII. An FID is always reported in two columns (real and imaginary components).
After you have displayed more spectra into the same window, in the form of overlays, you can create an ASCII table containing all the spectra synchronized (each spectrum in its own column) and normalized (each overlay is multiplied by its user-settable amplification factor). The frequency values are taken from the main spectrum (the one giving the title to the window). When an overlay has not a point at the same frequencies, its intensity is interpolated. When the digital resolution of the overlay is very different from that of the main spectrum (more than 100%), that overlay is not included into the table (you should change the number of FT points).
One-dimensional spectra and FIDs can be also exported as JCAMP-DX files. This is the standard endorsed by IUPAC to exchange spectral data among different computers and programs. This conversion requires a truncation of each data point to the lower integer. Before truncation, however, points are also pre-multiplied by a user-controlled factor. It turns out that you, the user, can adjust the degree of the truncation. In practice, if you magnify the spectrum (for example, pressing the '+' key one or more times) before creating the JCAMP file, your spectrum is less truncated. If you reduce the magnification the spectrum will be more truncated. The former case reproduces the noise more accurately, generates longer files and some line in it can contain more than the 80 characters (limit specified by the standard, irrelevant in most cases).
iNMR also reads JCAMP-DX files.
Bi- and Three-dimensional transformed spectra can be exported in the *.ucsf format required by Sparky. (UCSF stands for: University of California, San Francisco). Once in this format, your spectra can be visualized with CARA.
gzip tar Archive
This option/shortcut first saves the document then creates a “Gnu zipped” version of it. To achieve the maximal compression, only the data points and the iNMR-specific information are preserved. The intent of this option is to create a light version of a document for short-term use and for exchange over the net. For example, to send a problematic spectrum to the author of the program and ask his advise. This is not a valid option for long term storage, because the resulting archive will be recognized by iNMR only. The archive will always contain a single spectrum. For more advanced options you can find plenty of alternatives in the operative system.
Press the option (alt) key and the Export command becomes “Export All”. iNMR can generate a different text file for each open window, whose name will be from the window title + .txt (or + .csv). When generating these text files, iNMR will silently delete any older file with the same name at the same location.
The default delimiter for ASCII files is “tab”. You can alternatively choose the comma in the iNMR/Preferences dialog.
A bitmap image is a raw picture so easy to manipulate that you have no problem in exporting it to other applications/computers. It is not so sophisticated and powerful as PDF, but quite often brutality comes as an advantage. You can save the spectrum as PNG, JPEG, TIFF, BMP or PICT (all bitmaps) or in PDF (an higher lever description of the page). The size of the picture is equal to the size of the window times a “resolution” parameter. This user-settable parameter is stored inside the Preferences dialog (at the bottom-left of the panel called “Output”). At the right of it you find another parameter that controls the line width. You have complete control over the size, proportions, resolution and line thickness.
Example: your window is 500 by 300 points; resolution = 4 and thickness = 0.25. The bitmap will be 2000x1200, with resolution = 1 and thickness = 1. Everything has been multiplied by the resolution parameter, while the bitmap resolution is, necessarily, unitary. PDF is a special case: the resolution is arbitrary and you directly get the size and line thickness you have specified. If you scale the bitmap down 4 times, the resulting thickness will coincide with the numerical value shown in the preferences dialog, while the size will correspond to the window size.
To set the width and height you can use the console command paper(). To create a PDF file, use the Print command.