Fast determination of 90 degree 1H pulse
A new automation program determines the 90 degree 1H pulse automatically in
a few seconds for different power levels. It works best with samples with an
intense solvent peak. Simply type p90 in Topspin.
Note that the program also executes a 'getprosol 1H', i.e. the 1H and
gradient pulse lengths in the acquisition parameters of the current data
set are automatically updated.
Topspin License Problems
If you get the following error when trying to start Topspin on a data
station
FLEXlm FEATURE TOPSPIN1 License server does not support this feature
The solution is to set the BRUKER_LS_LICENSE_FILE environment variable.
Then logout and log in
#!/bin/sh LM_LICENSE_FILE='1700@carp.anu.edu.au' export LM_LICENSE_FILE /usr/local/topspin/topspinIf necessary, change the last line to the installed location of Topspin.
Software Upgrade (13 October 2004)
Peter Barron has recently done some work on the computer which drives the
800:
Currently available probes (July 2004)
TXI H / N / C probe with automatic tuning and matching.
TBI H / P / broadband probe with manual tuning and matching.
(BB tunes down to Rh).
Shigemi tubes:
Varian Shigemi tubes are not suitable for our 800 MHz NMR spectrometer,
because they have a too long segment of glass at the bottom. (The tube must
not be placed lower than what is indicated by the line in the plexiglas
sample-adjustment tube, since the temperature sensor in the probe is right
below.) Bruker Shigemi tubes have a shorter glass segment (in fact, too
short, according to Ralph Ruin) which allows the sample solution
to be centered in the rf coil.
Also, do not use "Varian length" Shigemi tubes in Bruker cryoprobes. There is some danger of doing some damage to the probe. Only use ones with "B" as part of the part number.
zz, multizz
GO, 7 June 2004
Always use zz instead of zg. zz is an AU program
from Rutger Folmer (Astra-Zeneca) which
- copies the current fid/ser file to the directory ~/dumpster,
i.e. one doesn't accidentally delete data so easily.
- copies the actual temperature parameters (flow rate, temp. setting,
correction factors) into the current data directory (file edte).
- copies the real pulseprogram in the current data directory.
multizz is like multizg, except that it uses zz
instead of zg and allows to do gradient shimming between queued experiments.
getprosol
Peter Barron, July 2004
The "getprosol" command is very useful once you have set up the pulse
program and channel assignments you want to use. It drags all the
pulse times/pulse shapes/ pulse powers from the prosol table that the
pulse program/channel assignements require. Note that pulse times for observe
and decouple 1H and 13C (i.e. f1 and f2) and decouple 15N (on f3) have
been entered in the table.
But what happens if your 1H pulse time (very likely) or 13C or 15N (less likely) are different to what is in the prosol table? The "getprosol" command can calculate new values on the fly.
i.e. getprosol <nucleus> <pulse time> <power>
getprosol 1H 9.2 -2.0
calculates all 1H pulse times relative to a 9.2 pi/2 @ -2.0dB and
loads 13C and 15N from table
getprosol 1H 9.2 -2.0
13C 11.1 -6
calculates both 1H and 13C, including all adiabatic pulses, and
loads 15N from table.
adiabatic pulses
Peter Barron, July 2004
At 800 MHz need to use adiabatic pulses for 13C so look for experiments
with "sp" in the name. "getprosol" will then load the default
shapes/powers/times. (If you are doing 1H-15N experiment which is
designed for doubly labelled samples, the pp name may not contain "sp",
even though it contains shaped/adiabatic 13C pulses, as this would imply
adiabatic 15N pulses. Note further that some pp's for 1H-15N experiments
have optional parts only performed if the sample is 13C labelled as well.
Whether this part is executed depends on the use of the zg options either
on the command line or the parameter ZG_OPTNS
i.e. "zg -DLABEL_CN")
The above getprosol commands do not set up for 13C adiabatic decoupling
which is essential for 800MHz.
After doing getprosol, check/set:
cpdprg2 = p5m4sp180
pdcp2 = 1.5ms
pl12 = 2-3 dB less than for garp (2-3dB < value called in by
getprosol i.e. 12-13dB)
spnam15 = Crp40,1.5,10.1
explist
CB, 28 May 2004
The Perl script explist lists all experiments in a directory.
Usage:
ssh, lsh
GO, 28 May 2004
The au-programs ssh and lsh store and load the current
shims in a file in the data directory. Great for retrieving shims, as they
tend to be sample dependent.
lpa
CB, 28 May 2004
The Perl script lpa lists the acquisition parameters in a
user-friendly format. It must be started in a shell at the directory level
of the experimental number (expno). For example lpa 3
Original program by Rutger Folmer. Modified by me.
ATMM Problem
GO, 15 May 2004
I noticed that after adjustment of the tuning and matching of the 1H
channel with atmm, the probe gets again vastly detuned after the first 1H
pulse applied. A second subsequent atmm provides stable tuning and
matching. The problem is specific to the 1H channel.
Temperature Problem
GO, 15 May 2004
Peter Caha broke the connection to the BTO2000. This means that the
temperature displayed in edte is ca. 20 deg. lower than the actual sample
temperature. I did a temperature calibration:
A setting of 278.5 K yields 25 °C.
A setting of 290.8 K yields 37 °C.
Position 5 of the sample changer now holds the Bruker temperature
calibration sample (ethyleneglycol with 20% DMSO). The program batman
allows an automatic (and very time consuming) temperature calibration.
For the Bruker temperature calibration sample (ethyleneglycol with 20%
DMSO):
| temperature | peak separation |
| 25 °C | 1.50 ppm |
| 37 °C | 1.38 ppm |
| 47 °C | 1.30 ppm |
Sparky
Joel Mackay, 28 April 2004
We have sparky running fine now. It is installed in
/opt/sparky and if you put
alias sparky='/opt/sparky/bin/sparky'
in your .bashrc file, you should be able to run it fine.
It allows to display the rrr files from Bruker 3D FTs.
Always leave some sample in the magnet!
GO, 21 April 2004
The sample changer requires that the
magnet is left open, i.e. no cap put on top. In order to keep dust
and dirt out of the probe, please make sure that there is always a
sample in the magnet.
Sample volume
GO, 20 April 2004
Ralph Ruin from Bruker recommended that
the top of the solution is at least 4 cm above the bottom of the NMR
tube to get good shims. This corresponds to 550 microlitres.
Shigemi tubes:
Frequencies, bf2, bf3, calibrate
GO, 20 April 2004
The basic frequencies for 13Cand 15N
were changed to 201.192313 and 81.076467 to yield o2p and o3p
parameters which are nearly correct (within 0.2 ppm). Bruker default
parameters reference to TMS instead of DSS (DSS is the commonly used
standard for aqueous protein solutions), resulting in about 2 ppm
deviation of the 13C frequency.
Accurate calibration values (namely the
chemical shifts of the carriers, assuming that the 1H carrier is at
the water frequency) can be calculated by the stand-alone program
calibrate which must be run in the data directory containing the
acqus file. It does not modify any files of Bruker.
File-extensions
GO, 19 April 04
Every user should put extensions on all
user-generated files (e.g. two-letter initials) which end up in the
common directories (pulse programs, shapes, parameter sets,
gradients). This will make it much easier for keeping track of the
files.
.bashrc, explist, pp, dd
GO, 19 April 04
Modify the .bashrc file to include your favourite aliases, paths and prompt. For a start, I copied mine, /home/go/.bashrc, to every user to give you a prompt that tells you where you are, alias pp to take you to the pulse program directory, alias dd to take you to your data directory, and access to the perl script 'explist -t' which gives you a listing of all experiments done including titles. More perl scripts will be added. This setup will also let you use $pp instead of /opt/xwinnmr/exp/stan/nmr/lists/pp and $dd for your data directory /opt/data/<username>/nmr.
The Avance 800 has finished its basic installation and acceptance testing, although the TBI probe has yet to be installed and the delivery of the Cyroprobe is still a number of months away. A loan TXI probe with XYZ gradients and ATMA is currently installed. The sample changer is operational. Hence the system is available for use, either locally or remotely.
sydney, unsw, wollongong
Each has the standard Bruker passwd for both login and vnc remote access. Please change these passwords on first login using the commands "passwd" and "vncpasswd". Each login has startup files for xwinnmr (.uxnmrrc and .xwinnmr-popeye/) and VNC (vncstart and .vnc/) installed.
| sx n | insert sample from holder n of BACS 60 sample changer | bsmsdisp | open shim and lock panel for manual shimming via mouse | atma | automatic tuning & matching ("atma exact" for best results) | atmm | manual tuning & matching via mouse | gradshim | gradient shimming - see later |
Currently there is a software problem that prevents tuning of 15N via the 15N preamplifier - no wobb signal is observable. To tune 15N requires a cable change BUT the 15N tuning is very insensitive and therefore does not need checking. To avoid problems, turn 15N on f3 to off in edasp before using "atma". This is not necessary using atmm, just change to 13C once the tuning window starts.
| 1D 1H | i1_z15_26 |
| 3D 1H | i1_shim12_26 (or i1_shim19_26 or i1_shim27_26) |
| 1D 2H | i1_z15_22 |
Note that it is not necessary to do 3D shimming on every H2O sample. However if it is done, it is then advisable to follow it with one iteration of 1D 1H shimming as this may produce a slightly better result for the on-axis shims.
| Nucleus | Pulse Time | Power | Comment |
|---|---|---|---|
| 1H | 9.6 | -2 | |
| 13C | 11.1 | -6 | |
| 70 | 10.1 | garp | |
| 12.1 | adiabatic decoupling (cpdprg2=p5m4sp180, pcpd2=1.5ms, sp15=Crp40,1.5,10.1) | ||
| 15N | 45 | -5.4 | |
| 180 | 6.6 | garp | |
| (Comment by GO: | 220 | 8.34 | garp yields perfectly fine decoupling with significantly less heating) |
Please do not
exceed these powers. It is recommended that, after setting
your pulse program name, pulse times and powers are loaded from the
prosol table via the "gpro" command. The prosol table has
1H, 13C and 15N pulse times, powers and shapes set, including all the
recommended 13C (use adiabatic with cpdprg2=p5m4sp180,
sp15=Crp40,1.5.10.1, pcpd2=1.5ms )and 15N (garp) decoupling values,
and the selective pulse shapes, pulse times and powers for 13C
selective excitation, adiabatic refocussing and inversion. All rf
channels and amplifiers have cortab tables so that linear behaviour
can be assumed. If you checked your 1H pulse time and find it has
changed, use gpro command with the following options:
gpro 1H <pulse time> <power level> i.e. gpro 1H 10.2 -2
which will recalculate all other 1H pulse times used by the current pulse program according to the hard pulse time and power. (There is a bug at the moment - gpro creates a file "prosol_History" in the current dataset but with permissions of r-r-r- or 444 which therefore cannot be overwritten by a subsequent gpro command. To repeat gpro, you will need to find the experiment number in a shell and delete the "prosol_History" file first).
Don't hesitate to contact me if you have any questions or encounter any problems in using the system.