Use the highest quality NMR tubes available from the stockroom.

Do not dry tubes in oven. Use air to blow dry instead. If you really need to use oven, set the temperature to below 100 degree C and place the tubes upright in a flask. Do not lay tubes flat on the rack.

Clean the outside wall of your sample tube with Kimwipes and alcohol before inserting it into the spinner turbine. Grab the top part of the tube so the grease and dirt on your fingers will not get onto the tube wall.

Hold the spinner by grabbing its upper part. Avoid touching the lower part of the spinner and the two white dots on the upper part. Clean the lower part of spinner with Kimwipes.

Lay the sample depth gauge flat on bench. Avoid dropping it to the floor.

**************Important notes about sample handling**************

========================

B. Commonly Used Commands

aa - abort acquisition

acqi - open the LOCK/SHIM window

ai - absolute intensity mode

aph - automatic phase correction

aph0 - automatically adjust 0th order phase correction

aphx - automatic phase correction

av - absolute value mode

bc - baseline correction using reset points

bpa - plot a box around the entire chart and parameters in boxes along the lower edge of the chart

cz - clear reset points

da - display arrayed parameters

dc - correct the linear drift of the baseline

dconi - display 2D spectrum interactively

df - display FID

dg - display acquisition/processing parameters

dg1 - display processing/ plotting parameters

dg2 - display decoupler parameters

dgs - display shims and other control parameters

dli - list integrals on the screen

dpir - display integral areas under the spectrum

dpf - display chemical shifts above peaks

dps - display pulse sequence

ds - display spectrum

e - eject sample

f - display full spectrum

ft - Fourier transform FID to spectrum

foldt - symmetrize 2D COSY-type spectrum

full - display spectrum across the whole window

ga - start acquisition and processing

go - start acquisition

i - insert sample

inset - display the section of spectrum selected by

two cursors as inset

isadj - adjust the largest integral to full scale

jexpn - joint experiment

nl - move the cursor to the nearest peak top

nm - normalized intensity mode

page - eject paper after plotting

pap - plot all parameters

pcon - plot contours

ph - phase mode

pir - plot integrals

pl - plot only spectrum

plcosy - plot COSY-type 2D spectrum

plhxcor - plot heteronuclear 2D spectrum

pll - plot line list

plot - plot spectrum and other graphics displayed

plot2d - plot any 2D spectrum

pltext - plot text

ppa - plot elected parameters

ppf - plot chemical shifts on peak tops

pps - plot pulse sequence

pscale - plot scale

pwd - check current directory

pwr - power spectrum mode

rn - recall display parameters stored with sn

ra - resume acquisition

region - automatic select peak regions for integration

rt - retrieve file

rtp - retrieve parameters

rts - retrieve shim values

sn - save display parameters as a set (n is the set #)

sa - stop acquisition

sd - set decoupler frequency

setlk - set lock parameters

su - set up hardware according the parameters

svf - save file

svp - save parameters

svs - save shim values

text - enter annotation

time - check total experimental time

vsadj - set the highest peak to scale

wft - weight the FID and Fourier transform to spectrum

C. Commonly Used Parameters

axis - unit of scale, p for ppm, h for Hertz

bs - block size

cr - the position of the left cursor

d1 - relaxation delay

delta - the distance between the two cursors

dm - decoupler mode

dmm - decoupler modulation mode

dn - decoupler nucleus

dof - decoupler offset

dpwr - decoupler power

gain - receiver gain

lb - line broadening

nt - number of transients

pw - pulse width

sc - starting position of chart paper for plotting

sp - starting point of the spectrum for displaying

sw - spectral width

th - threshold value for peak picking

tn - transmitter nucleus

tpwr -transmitter power

tof - transmitter offset

vp - vertical position of the spectral baseline

vs - vertical scale of spectrum

wc - width of chart paper for plotting

wp - width of plot for displaying

D. What's New

I. GOESY (Gradient-Assisted 1D NOE Experiment) - on INOVA spectrometers only

1. Take a normal 1H 1D spectrum.

2. Type goesy [ret] to load relevant parameters.

3. Use the two cursors to enclose the peak region to be irradiated, and click on the SelectH button.

4. adjust nt as needed and start the experiment by ga [ret].

II. NOESY1D (Gradient-enhanced 1D NOE Experiment) - a variant of GOESY

1. Take a normal 1D 1H spectrum.

2. Type NOESY1D [ret] to load relevant parameters.

3. Use the two cursors to enclose the peak region to be irradiated, and click on the select and the proceed buttons in sequence.

4. adjust nt and mix (mixing time) if needed, and ga [ret] to start the experiment.

III. Storing Spectrum As An ASCII File

1. Expand the region of the spectrum needed to be converted.

2. Type writespec(‘filename’) [ret].

(the filename is in the current directory, and contains only the value of the Y coordinate for each data point. Therefore, you need to jot down the starting and ending values of the chemical shift of the expanded spectrum.)

IV. 2D Base-plane Correction by Subtracting Rows

1. Display the 2D spectrum with dconi [ret].

2. Use the cursor to select a particular row that has only unwanted noises and artifact peaks. Note the row number (row #) displayed after INDEX: on the headline.

3. Type trsub(row #) [ret] and dconi [ret].

(If you need to do the same on columns, rotate the spectrum by 90 degree so columns become rows and apply the same procedure above.)

V. New plcosy command

plcosy(‘pos’,i,j,k,m)

‘pos’ -- plot only positive peaks; ‘neg’ for negative peaks; both if omitted

i -- number of contour levels

j -- intensity ratio of adjacent levels

k -- exp no. with good 1H 1D spectrum used for projections

m -- multiplier for changing the spectral amplitude of projections

VI. How To Use ZIP Drives For NMR Data Storage

(*Keep your ZIP disks > 7 feet away from the magnets to avoid data loss by the magnetic field.*)

a. Saving current data onto the ZIP disk

1. Insert your ZIP disk into the ZIP drive. (only IBM PC formatted disks can be recognized; you can use either 100MB or 250MB disks; each disk can hold up to 2000 1D files.)

2. Type mtzip [ret] (or click the File, then the mtzip buttons) to mount the disk.

(You can check the contents of your ZIP disk now by clicking on the File button again.)

3. Type svf [ret], and then enter the filename.

4. When done, type umzip [ret] (or click the umzip button) to unmount and eject the disk,.

*The disk can not be ejected without issuing the umzip command first.

b. Retrieving data from the ZIP disk

1. Insert your ZIP disk into the ZIP drive.

2. Type mtzip [ret] (or click on the File, then the mtzip buttons).

3. Click on the File button to display the filenames on the ZIP disk.

4. Click on the filename that you want to retrieve, followed by clicking on the Load button.

c. Copying files onto the ZIP disk

1. Insert your ZIP disk into the ZIP drive.

2. Go to your subdirectory, and click on the files (directories) you want to copy onto the ZIP disk.

3. Type cp2zip [ret] (or click on the cp2zip button), and wait until the task is finished (indicated by a refreshed display of the files in your subdirectory).

*cp2zip command automatically mounts the ZIP disk, and unmounts it when the task is finished. Therefore, do not use mtzip and umzip commands for this task.

d. Moving files onto the ZIP disk

1. Insert your ZIP disk into the ZIP drive.

2. Go to your subdirectory, and click on the files (directories) you want to move onto the ZIP disk.

3. Type mv2zip [ret] (or click on the mv2zip button), and wait until the task is finished (indicated by a refreshed display of the files in your subdirectory).

*mv2zip command automatically mounts the ZIP disk, and unmounts it when the task is finished. Therefore, do not use mtzip and umzip commands for this task.

*The files moved to the ZIP disk will no longer be in your subdirectory.

VII. HOW TO USE THE DS2 DATA STATION FOR OFF-LINE DATA PROCESSING

The DS2 data station is based on a SUN Ultra10 computer running Varian VNMR program under the account name ds2. It has a privilege of reading all the data stored in the spectrometer computers. These data are for reading only, and can not be deleted or modified. The directory in which these data can be found is /export/home/ds2/vnmrsys/data/(machine_name). You can read any particular fid file and do off-line processing using the DS2 data station. You can also copy any files to the local disks including the ZIP disk by following the same procedure as in using the spectrometer computers. If needed, you can access to the ds2 account remotely by using telnet from your own unix computer (please let us know if you want to do this since you need the password to login to the ds2 account).

To read a particular fid file stored in the spectrometer computer:

1. Click the DATA button, you should see a list of subdirectories with the instrument names (i500, i500b, i600, m300, m400, m400b).

2. Click the instrument subdirectory, and then the Set_Directory button to go into the group subdirectories.

3. Click on your group subdirectory, then the Set_Directory button, and look for your own file (or your own subdirectory, if you have one).

4. Highlight (click) your file to be read, then click on the Load button to load the fid into the local computer and you can do processing as usual.

To store your file onto the ZIP disk:

1. Insert your ZIP disk.

2. Locate the file(s) that you wish to store by clicking on the DATA button, then the proper directories until you see the list of your file(s).

3. Highlight all the files to be stored, then click on the cp2zip button.

VIII. HOW TO USE YOUR OWN UNIX COMPUTER FOR OFF-LINE DATA PROCESSING

A. Using telnet

1. Open a Shell window, type telnet nmrsun2, and enter the login name and password:

password: ********

(The password will be changed frequently, please check with us if you have problems logging in.)

2. you will be asked the following questions, which should be answered correctly:

Choose s)un x)window t)ek d)umb g)raphon [s/x/t/d/g(default)]: x

input display server name: (host name of your computer, e.g. slsiris)

3. When successful, you should get a prompt,

nmrsun2:ds2 1>

4. Type vnmr to start the NMR program, which should open the three familiar windows you usually see on the spectrometer computers.

(Note that in this way, you will be using the cpu and the printer of nmrsun2 computer.)

B. Running VNMR on your own computer

1. You can run the Varian VNMR program on your own unix computer. To install the VNMR program, please ask Bill Collins for the CDROM and Installation Instructions.

2. You need to use FTP to transfer your data from the nmrsun2 to your own computer.

(1). First, on your own unix computer, telnet to nmrsun2, as described in A.

(This step is ignored if you are on the nmrsun2 computer.)

(2). Go to the directory where your files are stored.

(3). Type

tar cf - ~/vnmrsys/data/filename.tar filename

This will convert your files (directory) filename into a single file under the name filename.tar in the /export/home/ds2/vnmrsys/data directory. This file can be transferred to your own computer via FTP.

(4). Type cd export/home/ds2/vnmrsys/data.

(5). Type ftp hostname of your computer.

(6). Enter the login name and the password of your account on your own computer.

(7). Go to your own directory on your computer.

(8). Type send filename.tar to send the tar file as a binary file to your own computer.

(9). Exit from FTP by typing the command bye.

(10). In a Shell window of your own computer, go to your own directory and type

tar xf filename.tar

which will convert the tar file back to a data directory that can be read by the VNMR program.