NMR data files

When you want to copy NMR data files from your hard disk to a floppy disk the easiest way is to use the My Computer. Double-click My Computer, find the file you want to copy, then click on it. On the File menu point to Send To and then click the drive where you want to copy the file or directory. You can again select multiple items by pressing and holding down the CTRL key as you click each item you want. 

Using WINDOWS Explorer select one of the 1D NMR data directories stored in the directory D NMRDATA GLUCOSE 1D and inspect the WINNMR data structure using the WINDOWS file manager (WINDOWS Explorer). Similarly inspect the data structure of one of the 2D NMR data files stored in the directory D NMRDATA GLUCOSE 2D. Check the processing number of the corresponding spectra. 

Select the directories D NMRDATA FORMAT DISNMR 1D H, D NMRDATA FORMAT DISNMR 2D HH and D NMRDATA FORMAT DISNMR 2D CH and inspect the structures of the NMR data files using the WINDOWS file manager (WINDOWS Explorer). 

In principle any NMR data file may be transferred and stored on your PC hard disk in its original format (UXNMR/XWINNMR, DISNMR). Alternatively the NMR data file may have already been converted into the WINNMR format on the remote computer before being copied to your PC. The most usual way, however, i.s to import the file in it.s original format and to convert it into the WINNMR format prior to using ID WIN-NMR or 2D WIN-NMR. 

In the subsequent Check its the transfer and conversion of ID and 2D NMR data files in the UXNMR/XWINNMR format is demonstrated using various alternatives. The converted data files will be stored and will be at your disposal for later processing in chapter 5. 

If you have installed the NMR data on your hard disk, assume that your CD-ROM disk (denoted E ) is now a NFS mounted remote disk. Start the 1D WINNMR program and from the File pull-down menu choose the Open option to read in a ID NMR data file in the UXNMR/XWINNMR format. The Open dialog box appears on the screen. Select the directory E NMRDATA FORMAT XWINNMR 1 D H HUX on your CD-ROM disk, and mark the... 

For ID data files three possibilities using the Open, Filecopy Convert or File Transfer ID WIN-NMR commands are available and the procedures are the same as described above for UNIX format NMR data files. 

The primary use of NMR is in the determination of the structure of unknown organic compounds. It is often used in conjunction with other spectrometric techniques (FTIR and mass spectrometry, for example) in this determination. NMR spectra are molecular fingerprints, however, and by comparison with data files of known spectra, the structure of an unknown can be determined independent of other data. 

Fig. 2.9 shows the main directory structure and the structure of two subdirectories of the NMR data base stored on your CD-ROM as displayed by the WINDOWS File manager. If it is planned to copy the NMR data from your CD-ROM onto your hard disk to speed up further processing, the same directory structure should be established there (see 2.5.5). Note, however, that ID WIN-NMR generates additional auxiliary subdirectories (AU, DAT, NMR, PC, TMP) in the directory DEMOID on your harddisk. 

The file names, e.g. GHHCODF, of the NMR data sets as shown in Fig. 2.7 and stored in the subdirectories C, H, IDREF, CH and HH include information on the sample, the type of spectrum (1D/2D) and the experiment itself. The meanings of the various ubbreviation.s are listed below ... 

Start the WINDOWS Explorer and check there is 150-200 MBytes of space available on one of your hard disk(s). Follow one of the standard procedures for copying files from one to another directory. Consult the WINDOWS manual, or first study the Check it instructions for copying a file or directory given in the next section (2.5.6), if necessary. Select in your CD-ROM the directory NMRDATA or any of its subdirectories and copy it to disk D on your PC. The directory NMRDATA GLUCOSE 1D H and a few auxiliary directories therein (see 2.5.4) have already been created during installation of ID WIN-NMR. Answer the corresponding question for overwriting all files stored under the same name with yes. Use the WINDOWS Explorer) to inspect the newly created NMR data directory NMRDATA on your hard disk. Click on several items in this directory and familiarise yourself with the directory structure. 

Data in either format must first be converted into a form that WIN-NMR understands before any processing steps may be performed with either ID WIN-NMR or 2D WIN-NMR. ID WIN-NMR and GETFILE include tools for converting both data formats into this WINNMR format. 2D WIN-NMR converts 2D data files in the UXNMR/ XWINNMR format - but not in the DISNMR format - automatically (see section 2.7.2). 

When NMR data is converted into the WINNMR format it is converted into a number of files stored in a directory called . For ID- and 2D WIN-NMR, the directory has the following structure ... 

Note . IR and. RI are only present if the spectrum and the corresponding experiment is phase sensitive (see section 3.4). Additional files such as. PLT,. T1T,. TI2 etc. may appear with your NMR data and contain additional information concerning the plotiing parameters, the spectrum title etc. 

NMR data measured on a modern Bruker NMR spectrometer (DMX, DRX, ARX) is stored as a directory in the UXNMR/XWINNMR format. Under the UNIX operating system, data files stored as are themselves directories. 

Additional files, FORMAT.TEMP, PULSEPROGRAM, VDLIST, TITLE, OUTD, PARAM.TXT, META and others may also be present if you have imported your NMR data directly from a Bruker spectrometer. These files contain additional information and settings initialized by the spectrometer operator and relate to the acquisition pulse program, lists of variable delays, spectrum title, the spectral layout and others and are non-essential for off-line data processing. 

Start the 1D WIN-NMR program by clicking on the corresponding icon. From the File pull-down menu choose the Open option and select in the dialog box the directory D NMRDATA FORMAT XWINNMR 1D H HUX. Check the UNIX symbol UX (in red) in front of the filenames in the selected subdirectory. Do not click on any of the data files in this moment, but use the Cancel key to leave this dialog box. 

In principle there is no label, if not set by the user, to identify the given DISNMR file as an FID or spectrum, or if the NMR data is from a H or C experiment. However the Bruker automation software, primarily developed to connect older type spectrometers (AC, AM) to a sample changer, allows the user to structure the name in such a way that it carries additional information with respect to the type of experiment. The user is referred to the corresponding automation manual available from Bruker and to the name conventions set by the key NMR operator at your site. 

Start GETFILE and inspect the various dialog boxes available in the File pulldown menu for conversion of NMR data formats of other manufacturers into the WINNMR format. 

If you have installed MAPI (mail application interface) software on your PC, you may exploit the MS-WINDOWS mailslot-function to e-mail NMR data directly to and from your PC. The full version of ID-WIN-NMR allows you to export/irnport FlDs, spectra, tables, text-files, relaxation data and metafiles to/from other users of (the full version of) ID WIN-NMR. Both JCAMP-DX5 and Bruker specific binary format are supported. Compared to the procedure outlined in section 2.6.5 this is an even more convenient way for exporting/importing NMR data via Internet. For further details refer to the ID WIN-NMR manual [2.1] or contact your Bruker/Spectrospin representative. 

For automatic data transfer and data conversion choose the Open option from the File pull-down menu in either ID WIN-NMR or 2D WIN-NMR in exactly the same way as for data files already stored on your PC hard disk. Open directly transfers and automatically converts (UXNMR/XWINNMR-data) ID or 2D data sets and shows the NMR data in the corresponding WIN-NMR application window for immediate processing. The processed data will not automatically be stored in the WINNMR format. 

The NMR data will be converted and will automatically be saved in the WINNMR format as C DEM01D DAT ASP3000 HDIS 001001.FID, but may also be stored under another name using the Save as. .. option in the File pull-down menu. Make sure that the binary format has been selected in the dialog box appearing on the screen and click the OK button which will initialize the save operation. 

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