NMR manager
Johns Hopkins School of Medicine
312 WBSB
Department of Pharmacology
725 N Wolfe St
Baltimore, MD 21205

410-502-4803(Office)

Basic proton 1D

1. log in ( use CDE environment by pointing to session and picking the CDE option before log in)
2. click on acqi button to open the acquisition window and click eject to eject the standard
3. use the depth guage to correctly place your sample into the spinner (bottom of tube flush with bottom
of guage) and then insert the sample, click insert in the acqi window. Alternatively, one could type e
in the macro window to eject and i to insert.
4. No need to lock, just close that window.
5. click GLIDE on the top macro, then click Set Up then pick the type of exp you want to run, eg, 1H, 13C, 31P...
8. In the GLIDE window, leave autolock autoshin as YES and click setup button.

9. Click Acquire button on the new popup window. The 3rd window pops up.

10. Click Do button. Now wait and see the plotter and get your spectrum. You do not need to do anything.

Advanced USERS:

type wft   aph see see your spectrum. zoom into the solvent peak to see if the shim is good enough. then change nt to 16 or 32 to collect your spectrum.

pl pscale pap page - this command prints your spectrum with a scale and the experiment parameters, not with
integrals. Useful printing commands:
pl = plot spectra (p. 413)
pscale = plot scale below spectrum or FID (p. 442)
pap = plot of all parameters (p. 385)
pir = plot of integral amplitudes below spectrum
ppf = plot peak frequencies over spectrum
dpf = display peak frequencies over spectrum. To do this you need to click th (threshold) and move the red line to where interested peaks are selected.
To name you spectrum, example: text(‘DJM-01-95’) To plot your text in the upper left hand corner type pltext.
To set the peak threshold, press the Th button in the menu and adjust to the appropriate threshold.

Printing integrals:
To print integrals under your spectrum you need to set the vertical plot value to 12 or higher, therefore you must
type vp=12 or 20 or a higher value. To print with integrals type pl pir pap pscale page

Integration:
Click the partial int button (that button can be full int or no int depends on how many time you click), and then  type cz and then click reset  button and use the mouse to click on either side of the peaks (left click). To undo, use right mouse button.
Type dli to display the values for the integrals and then type setint(peak#, value#) to set a certain area to a
particular value. A list will be displayed listing peak areas from left to right. If you wish to set the number of
protons of a particular peak, choose the peak# from the list. For example, if the second resonance is equal to 2
protons, type “setint(2,2)”. Type “dpir” to display integrals under spectrum.

Reference a peak:
Place the cursor at the peak you want to reference and then click at the reference button and you will prompted
to enter the ppm value to which you want to set the peak. One can also type rl(0p) to reference selected peak to
0 ppm or type rl(7.26p) to reference to 7.26 ppm. To place your cursor and the peak to be referenced, the nearest
line, “nl”, command is useful.

Defining width and start of scale:
When comparing different spectra, it is useful to have them all on the same scale. Instead of “eyeballing” it, you
can use the width of plot, “wp”, and start of plot, “sp”, commands. For example, typing wp=10.5p sp=-0.5p will
give you a scale starting at -0.5 ppm and stopping at 10 ppm. The total width of the plot is 10.5 ppm. To change
scale axis from ppm to Hz, type axis='h’. To change it back to ppm type axis=‘p’.

Saving Data:
In order to transfer data via FTP, you must first save your data on the NMR computer hard drive. To save data,
type svf then hit enter. You will be prompted to enter a file name which cannot include special characters. Hit
enter.

Retrieving Data:
To retrieve data, click the main menu button, the click file and then data. A list of your files will appear. If you do not see your fids, then click select directory, and then click home. You should see all the files at your own home. Select the fid you want using mouse and then click load and then type wft.