This document is designed to help users of SpecNMR. Select the topic below you want to read more about.
SpecNMR requires a PC (386 or above) with mouse and colour monitor running Windows for Workgroups connected to the chemistry network. A Windows compatible printer (inkjet or laser) is useful. If your PC has not had the software installed, please see Dr. Murray.
SpecNMR will process and display 1-dimensional NMR spectra from any of the JEOL spectrometers in S100. It will not process 2-dimensional spectra, and it has very few automation procedures (at present).
The spectra you require to process must be readable by the PC. Currently this requires using FTP (file transfer protocol) to transfer them from the spectrometer to your PC The following steps are required for Lambda data.
GX270 data is transferred to the SpecNMR PC in S100 by the NMR technician after you have requested a transfer using the @KEEP program on the GX270.
GX400 data must first be transferred from the GX400 to the Lambda.
Log in to the Lambda using telnet from your PC, with userid and password as in 3 above. You will get a bash$ prompt. Type cd data/gx400. Type ftp gx400, then give your GX400 username and password. Type binary, then get mm1234.gxd (for filename MM1234). Repeat for other files you require. Then type ascii, then get mm1234.gxp. Repeat this for other files, then type quit to return to the Lambda. Type exit to log out from the Lambda, then close telnet.
The .GXD files may now be transferred from the Lambda (where they will be in the directory data/gx400) to your PC as above, but you must also transfer the .GXP files as well, having first selected transfer mode 'Text (ASCII)'.
Alpha 500 data (in *.nmf files) can be transferred as Lambda data. See Dr. Murray for userid and password. Before transfer a *.TXP file must be created on the Alpha, then transferred as a text file like GXP files from the GX400.
Start SpecNMR by double-clicking on the SpecNMR icon on your Windows desktop.
From the File menu, choose Open, then select the drive and directory where your Lambda .nmf file is located. The FID should be displayed in a window.
This will be more familiar to GX users as the window function. From the Apodization menu choose Exponential (for 1H spectra) or Gaussian (for 13C spectra). Set BF to about 0.3 Hz (1H) or 0.5 Hz (13C), GF to 1 Hz (13C). Choose Apply. If there is still signal at the right hand side of the FID (usually not the case with Lambda 1H spectra), choose Trapezoidal from the Apodization menu. Ensure that T1 = 0, T2 = 0, T3 = 90, and T4 = 100, then choose Apply. Alterations to BF and GF can be used to enhance resolution or sensitivity.
Then from the Process menu choose FFT + Phase. Increasing Point will results in zero-filling, which is desirable for GX270 data. Then choose OK. The Fourier transformation will take a few seconds, depending on the speed of your PC.
Buttons to increase or decrease XE or YG (in powers of 2), or to do All Reset, are available on the toolbar. Additionally, the left mouse button provides an XYZoom function (at all times). A double click of the left mouse button does All Reset. Ctrl Z will undo an XYZoom, Ctrl A will redo an undone function. XShift and YShift functions are available via the Windows scroll bars.
An increased YG is helpful for phasing. Adjust P0, using the scroll bar (and selecting x10, x1, or x0.1 for greater or less sensitivity) or arrows to adjust the phase of the marked peak. An alternative peak may be selected with PP and the right mouse button. Then adjust P1 for peaks away from the main peak. Values of P1 should be consistent for spectra from the same instrument run with the same menu. When the phase is OK select Apply.
From the Process menu select Calibrate. Place the cursor over the TMS peak (if visible, otherwise select a solvent peak) and press the right mouse button. Then enter the shift of the peak selected (e.g. 0.0 for TMS) and hit OK. For heteronuclear spectra (31P etc.) set the calibrate peak to the centre of the spectrum (8192 or 16384) by X expanding several times and checking off the "Set to nearest peak" function. Then enter the known shift (e.g. 0.0 for P menu on GX400).
You will probably have noticed when phasing a 1H spectrum that the baseline is not perfectly flat. This baseline 'roll' will affect integrals, and is quickly removed. From the Process menu select Baseline. Increase YG somewhat to show the 'roll'. Use the right mouse button to select points on the baseline which should be 0. Then select Show, to see the effect, or Apply when done. Baseline correction is rarely necessary for 13C spectra)
From the Analyze menu select Integrate (1H spectra only). The integral that appears initially will disappear. Integral blocks are selected by drawing a box with the right mouse button. A started block can be cancelled by making the block of zero height. Slopes at the start and end of integrals can be corrected with the right mouse button, but should not be present if baseline correction has been performed. A selected block can be referenced to a chosen value, or deleted with Ctrl X. IYG changes the gain of all blocks (preferred), the gain of individual blocks can be changed (but not recommended). The integral values of blocks cannot be printed on the plot, but can be displayed and printed separately with Analyze List Integrals. When integration is complete, hit OK.
Selecting Peaks from the Analyse menu allows peak picking. Initially, with TH, NL, and BA all set to zero, >512 peaks will be selected, and none shown. Increasing TH and NL will decrease the number selected. Only peaks above TH are selected, NL serves to discriminate noise from peaks. BA should be zero if baseline correction has been done. Selected peaks are shown by little black markers, but peak shifts and frequencies are not shown on plots. A list of selected peaks can be shown by Analyze List Peaks, and printed from that window.
Under the File menu, Print Setup allows the choice of landscape or portrait settings, printer, etc. Print then gives a dialogue box in which features can be selected (x in the box), deselected (clear the box) or plotted if displayed (grey box). The plotting size should be appropriate to the format selected. Suggested is 20 x 15 for landscape, 15 x 10 for portrait.
Under the Options menu you can set various preferences for display. These will originally have been set to sensible values, but may be changed if required and stored (along with some other parameters like plotting sizes) with the Settings option.
Spectra displayed in SpecNMR can be easily pasted into a word processor, using Copy to Clipboard from the Edit menu. The size of the pasted image depends on the size of the window. Pasted images can be subsequently resized in the word processor, or edited with MSDraw, though the latter is not particularly recommended.
The F1 key gives access to context-sensitive help at all times. Copies of the manual are available at major processing sites. Advice on features of SpecNMR can be obtained from Dr. Murray, Dr. Torren Peakman, and the NMR technicians. An updated version, with additional features, is expected in the new year. The current version of this document is available on the World Wide Web at
http://zeus.bristol.ac.uk/~comm/specnmr.html
This version updated 17.10.96