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Bruker Avance 300 – Basic instructions for Xwin-nmr
computer name: SPIN300
Frequently asked questions are listed at the end of the document
step one: FIRST pass the NMR exam on the AC200s !!
1. Login and open the program
Sign the logbook.
To see the user login i.d. if the screen says to press the ctrl + alt + delete
buttons, press all three buttons at the same time.
Check which probe is in the magnet.
? 29Si probe, the user name is: qnp29Si
? 19F probe, the user name is: qnp19F
The password for either probe is:
To open the Xwin-nmr program double click on the desktop icon.
2. Create a file location for the data
dir <enter> choose a location for your experiment
edc <enter> choose an experimental number
you can also use the pulldown menus: File Search . . . to find
your directory and expnos (experiment numbers).
3. Read in experimental parameters
named by probe and solvent:
for example:
19F probe: rpar cdcl3-f <enter>
29Si probe: rpar cdcl3-si <enter>
select “copy all” with the mouse
t <enter> type your title then save and exit
4. Insert the sample:
Put the sample into the blue spinner with the yellow stripe
Check that the depth measure is set to 2.
Wipe the outside of the NMR tube with a clean cloth
HOLD THE SAMPLE BY THE TOP
BSMS keyboard: press “lift on/off” (green light is on)
WAIT for the air (you should hear it and feel it)
Set your tube with spinner on the air cushion
press “lift on/off” (green light is off)
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5. SPIN (optional):
BSMS keyboard:
press “spin” (green light on)
to check the spin rate: orange 2nd button + Spin measure/Spin rate
to deselect: std-by
6. LOCK:
Check which probe is in the magnet and read in the appropriate shim file:
? 29Si probe, type:
rsh qnp29si <enter>
? 19F probe, type:
rsh qnp19f <enter>
To LOCK, type:
lock <enter> & click on solvent
To open the lock display window, type: L <enter>
Adjust “lock phase” (BSMS keyboard) to maximize the lock signal
7. Basic SHIMMING:
BSMS keyboard - light the following buttons:
“FINE”
“ONAXIS”
“Z1” and turn the knob to maximize the lock signal intensity
IF THE LOCK SIGNAL GOES TOO HIGH, REDUCE LOCK GAIN
“Z2” and turn the knob to maximize the lock signal intensity
“Z1” ditto; keep maximizing:
Z1, Z2, . . . Z1 until no further changes
“STD BY”
Instructions for shimming on the fid or spectrum are on page 8.
More shimming (optional):
TURN OFF THE SPINNING
“X” and “Z0” and turn the knob to maximize the signal intensity
“Y” and “Z0” and turn the knob to maximize the signal intensity
“STD BY”
8. Acquire a FID:
a <enter>
moves to the acquisition mode window
rga <enter> receiver gain, automatic - sets the amplification
ignore the window that says –2/100 . . .
to see if rga is or is not actively running:
Display Active Commands  Show
(if it’s not on the list, then it’s not running)
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ns <enter> number of scans (there is no –1, but 11k is a lot)
zg <enter> if you don’t see an FID, GET HELP
More options to try while the fid is aquiring:
To view an fid while the experiment is still running:
tr <enter> will save the acquired transients to the memory.
you can ft while the acquisition continues.
To halt the experiment before it reaches ns:
h <enter> will halt the acquisition AND SAVE your fid
To add more acquisitions to the fid after it has halted:
go <enter> will “go” without first deleting the memory
9. Fourier transformation:
in Xwin-nmr (PC keyboard) type: ft <enter>
Window functions can also be applied to the fid, for example:
sensitivity-enhancement (lb > 0), type: ef <enter>
resolution-enhancement (lb < 0, gb > 0), type: gf <enter>
you can also type “winfunc” to see the effects of the functions
10. Mouse manipulation – basic buttons on the screen
buttons on the left:
*2 and *8 increase the vertical display
/2 and /8 decrease the vertical display
“all” shows the entire spectrum (analogous to <ctrl> R)
“plot reg” shows the defined plot region (analogous to <ctrl> F)
left-mouse connects to spectrum or releases
middle mouse selects (similar to “R” or “Z” on AC spectrometers)
so, to expand with the mouse: Left, middle, middle, left.
11. Phase
for automatic phase correction type: apk
for manual phase correction:
use the mouse to left-click on the “phase” button
left-click on “biggest”
hold the mouse over ph0, drag the left-mouse (zero-order phase)
hold the mouse over ph1, drag the left-mouse (first-order phase)
to save and exit: left-click on “return” then “save and return”
12. Baseline correction
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for automatic baseline correction, type: abc <enter>
for manual baseline correction type: basl
13. Define plot region
use the mouse to select the plot region on the screen
left-click on “dp1” (left-side of screen) to define the plot region
F1 is the left side of the spectrum <enter>
F2 is the right side of the spectrum <enter>
Change the spectrum y-scaling on display? y <enter>
(if you see a warning that the scale changed, click OK)
If you do not click on the dp1 button on the screen, the plot region
will not be updated in the computer’s memory.
14. Integration
left-mouse click on “integrate”
left-mouse click to adhere to spectrum
middle-mouse click to define integration regions
use the buttons on the screen to expand & move the spectrum
note options for “current” or “all”
to select a peak for “current” double click on the integrand symbol
to calibrate the area value of a peak – select it (see above) and click
on “calibrate”
to save and exit:
left-click on “return”
“save as an ‘intrng’ and return”
To view the current intrng file – enter the integration mode
With the mouse, go to the pull down menu at top of screen:
File  Read “intrng”
15. Peak picking
click on “utilities”
click on “YU” (until the y-axis units are in cm)
click on “CY” define the top of the spectrum as 11 cm
if you get an error message, type: pscal global <enter>
click on “MI” define the cut-off for peak picking
use left-mouse to place blue-bar across the minimum intensity
you can also just type values for CY and MI,
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for example:
CY <enter> 11 <enter>
MI <enter> 0.5 <enter>
16. Plotting
v<enter> to view your plot
click on quit
to make changes, type “edg”
edg gives an array to change plot parameters
v<enter> again, until satisfied with spectrum
click on quit and either make changes in edg again, or “plot”
type plot to get a hardcopy
17. Send your data to Nmrlab1 or your lab computer
Minimize the Xwin-NMR window
Open the SPIN300 file icon on the desktop (double-click)
Open the Network Neighborhood icon  Nmrlab1  data 
directoryname  nmr 
Drag and drop files from SPIN300 to Nmrlab1
!!!Files must be in the correct folder pathway (“tree”) to be readable.
PLEASE NOTE – ANY DATA LEFT ON THE SPECTROMETER
COMPUTER IS SUBJECT TO DELETION WITHOUT WARNING.
To open Xwin-NMR files on the remote computer:
a. open the program Xwin-NMR
b. use the pull-down menu: File  search . . .
c. click on the appropriate user to open the file, apply, and close
18. Remove your sample
turn off: spin and lock (no green lights)
on the BSMS keyboard: press lift on/off (green light on)
gently lift your sample up
press lift on/off (green light off)
FAQs / troubleshooting:
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In XWIN-NMR the blue bar at the top shows a different group is logged
in. How can I change user?
First you need to exit all programs. To exit XWIN-NMR, go to the pull
down menu and check what programs are running: Display  Show
active commands. Check that zg is not running. Click OK.
If no experiment is in progress, type “exit” and click OK in the window.
Second, logoff the current NT user. From the Start button in the lower left
corner of the screen, click with the left mouse button and choose “shut
down” from the menu. Make sure the third option in the new window is
highlighted  close all programs and log in as a different user  click
OK.
I type a command in Xwin-nmr and nothing happens.
Use the mouse to left - click inside the pink command line.
(Beware the “tab” button that deselects the command line. If a second
window is open (ex. “lockdisp”), you’ll need to move xwin-nmr to the
forefront.)
There’s a robot in the way of inserting my sample.
Lift the robot STRAIGHT up by the handle, and set aside in a safe place.
How can I check the value of the parameters in my file?
ased <enter>
gives a table of the relevant acquisition parameters
as <enter>
gives each relevant acquisition value, one at a time
eda <enter> gives all acquisition values, relevant or not
edg <enter> gives a list of plot parameters
edp <enter> gives a list of processing parameters
edasp <enter>
gives a graphic display of the nuclei/amplifiers in use
Can I adjust the baseline manually?
Yes, type basl <enter> and use the mouse to fit the line on the screen to
your baseline.
This is the similar to “k” in EP mode on the AM/AC spectrometers.
Can I do a “splines” baseline correction, like I usually do on the AM/AC
spectrometers?
Sure. Go to “utilities” (click with the mouse from the left-hand menu).
Click on “def points” and use the middle mouse to define points on the
spectrum – you’ll get a small green arrow at every selected point. Click
with the left-mouse once. Type sab <enter>.
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How do I measure a 13C spectrum?
dir <enter>
choose a location for your experiment
edc <enter>
change the experiment number - optional
read in experimental parameters (named by probe and solvent):
rpar <enter>
you will see a list of possible experiments
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For a H parameter set choose the solvent and probe type, for example:
19F probe: rpar cdcl3-f <enter>
29Si probe: rpar cdcl3-si <enter>
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For a C parameter set choose (de)coupled and probe type, for example:
19F probe: rpar 13C_decoup-f <enter>
29Si probe: rpar 13C_decoup -si <enter>
NOTE: the rpar list is arranged according to capital letters first, then
lower case letters, and finally numbers. You will need to scroll all the
way to the bottom of the list to find the experimental parameter set
options for most X-observed experiments.
THE FIRST TIME YOU WISH TO RUN A NON-1H EXPERIMENT,
PLEASE ASK FOR ASSISTANCE – IT WILL ONLY TAKE A FEW
MINUTES AND WILL PREVENT MOST MAJOR MISTAKES FROM
OCCURING – THANK YOU! Yael 3748.
The acquisition looks finished, but the window only shows n-1/n shots?
Software bug. Ignore and go on to fourier transformation.
I used “halt” to stop the acquisition, how can I check how many
transients were averaged?
Type: 2s ns <enter> in the command line.
How many ways can I change the experiment number?
1. with edc
2. type: re 2 <enter>
to go to experiment number 2, etc.
3. type: iexpno
4. type: ix
5. File  Search . . .
6. type: search
I “stopped” the acquisition with “stop” instead of “halt,” where’s my
FID?
Sorry. You must use “halt” to save the acquisition. If you used tr earlier,
you’ll at least have saved those scans.
Can I run multiple experiments on the same sample?
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Yes, set up a series of consecutive experiment numbers. rpar the
appropriate parameters into each experiment. Go to the first experiment
number in the series and type: multizg. The computer will ask how many
experiments, and then run each of them in turn.
You can also use icon-nmr (with OR without the robot) to run
multiple experiments.
How can I check how long the experiment will take?
Type: expt <enter>
at the command line. This will give you a window with the calculated
amount of time needed for the experiment (approximately equal to
(aq+d1)*(ns+ds)). You may increase or decrease ns to make the
experiment time longer or shorter, respectively.
How do I shim on the 1H fid (or spectral line)?
(i) FIRST COMPLETE STEPS 1-6!
(ii) Check to see how long it takes to refresh the screen:
aq <enter>
d1 <enter>
aq+d1 should be ~ 2 seconds for comfortable shimming
to make aq faster: make td smaller or sw larger
to make d1 faster: d1 <enter> 0.2 <enter>
(iii) Take one scan and phase the spectrum
rga <enter> wait until rga is finished
ns 1 <enter>
ds 1 <enter>
zg <enter>
ft <enter>
apk <enter>
(iv) enter the go-setup mode
a <enter>
gs <enter> wait for the RCU and TCU until it’s acquiring
frq <enter> to shim on the spectral line
tim <enter> to shim on the fid
shim on the BSMS keyboard: Z1, Z2, Z1, etc.
(v) stop
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