Bruker Avance 600 Status Reports
This is a cumulative index of status reports for the Bruker Avance600 spectrometer. You can
find important information here about hardware and software updates, any known problems that
might exist, or recent changes in the instrument configuration that you should be aware about.
Topics are listed starting from the most recent posting. If you are looking for information
on a specific topic, use the find command on your browser.
"edc" bug. Bruker has reproduced the "edc" bug
(inadvertant permission error that occurs
when edc is used to copy a data set) that occurs under version 3.1 of the
software (which is now running on all of our spectrometers).
Thus, if you see this error, its just a bug a can be safely ignored.
A fix for this will be issued in version 3.5 of the software which will be
released in about a month from now.
7/30/2002, 1H Pulse Issue Resolved, XWIN-NMR 3.1 Upgrade, New UPS Supply for Host Computer
1H Pulse Issue Resolved. The 1H pulse issue on the Avance 600 QXI probe
has been resolved.
The problem turned out to be a bad capacitor on the 1H channel.
Two pieces of information led me to conclude that the probe was in fact the
source of the problem: longer pulse widths and lowered signal-to-noise.
In a situation with a long 90 degree pulse, there are really only two possibilities,
the transmitter or the probe. A
transmitter problem would give longer pulse widths, but should not influence
the signal-to-noise. A probelem with the probe, however, explains both.
One thing that did not make sense was that the probe tuning curve looked
fine. For this reason, I was initially less suspicious of the probe.
Current pulse widths are posted.
New UPS Supply for Host Computer. The SGI host computer for the avance600
has been changed from a low capacity UPS to the UPS system that is used to supply
electrical power to the NMR consoles. This is a big improvement since the low capacity
UPS previously used was only capable of holding the computer for about 10 minutes (which
obviously caused problems during extended power outages). The UPS system that supplies NMR consoles
(and which now supplies the SGI host computers) is much more reliable in this regard since
it a) has a much higher capacity and b) because it is wired into the buildings emergency
power system. Thus, in an extended power outage situation, the UPS will initially hold
the spectrometers and computers via its large internal batteries. After about 2-3 minutes,
the buildings emergency power will become active (comes from a large diesel generator located
behind the building), which will then supply the UPS and rechage its batteries. After normal
power has been restored, the UPS will handle this switchover as well. NOTE, that this change
applies to all three NMR spectrometers, not just the Avance600.
XWIN-NMR UPGRADE TO VER 3.1 Patchlevel 11. The XWIN-NMR acquisition control
software has been upgraded from version 3.0 to 3.1 (patchlevel 11). As best I can
tell, the operation of this version of the software does not change anything
with regard to current operating procedures (Yeah!!). The motivation for upgrading
the software was a bug (discovered by trial and error, but noticed in other labs as well)
in which 2D processing would cause the computer to completely hang.
7/16/2002, Data Disk Renamed, Network Printer, Processing Bug
Data Disk Renamed. To maintain consistency
with other computer setups in the nis cluster, the data disk on avance600
has been renamed from /avance600 to /avance6001. Note that the read-only
mount onto the nis cluster has also been updated to /avance6001. The only
major consequence of this that users will need to deal with is how the
data directories are displayed in the portfolio editor. Thus, in
topspin open File ---> Search, then choose "edit" to modify the data
disks availabe to include /avance6001 and to exclude /avance600. Once
complete, go to the File menu on the portfolio editor and click "Save
Printers: The nmr facility now has its own printer. Its on the lab bench
in the 700 room. This is the only printer setup from within topspin. To use
it from within topspin, type "edo" on the topspin command line (edo stands for
edit output device - this in essence tells topspin which printer you want
to use). This will bring up a dialog box. For the CURPRIN and CURPLOT entries,
you should choose hpclj. For printing spectra you can use the "plot" command; for printing
parameters you can use the "lpa" command. See the topspin manual for more
details on these commands. Note that the nmr facility laser printer is also
accessible from the unix command line. Here you should refer to the printer
as laser2 (for example to print a text file, lp -dlaser2 my_text_file.txt).
Processing Bug There is a bug in the current version of topspin 3.0
which causes sgi o2 to completely hang (not always, but often) when 2d data is processed
while an acquistion of some sort is in process (not always, but often). In order
to recify this problem, we will soon be upgrading the spectrometer to topspin 3.10. In
the meanwhile, if this happens, you can use the following procedure to rectify the problem:
1) Remove the power cord from the rear of the sgi (this is a drastic step and
should not be used under normal circumstances).
2) Replace the power cord and Power the sgi back up (hit the button on the lower left).
3) Once booted, log in, open a shell, and type "telnet spect". Login in as root (hit return
return when prompted for password) and then issue the command "init 0". This will shut down
the acquistion computer on the console and halt the current acqusition.
4) Open the middle cabinet door of the avance600 console, and press the red reset button
on the top left (its on a board labeled "ccu"). This will restart the acquistion computer.
5) Go back to the sgi. From a shell, type "telnet spect". If you are able to login (as root),
then the acqusition computer is up. If not, you may need to wait 30 sec or so longer to give it
time to boot. Once you've successfully logged into spect, type "exit" to exit.
6) Now, start xwinnnmr. Once running, type the command "cf". This will ask you many questions -
answer the default for all of them. Also, it is to be expected that error messages will
be presented. This is normal on the first pass through cf after a reboot. Once complete, run through
cf again. This time you should get no error messages. You should now be ready to resume your
7/10/2002, 1H pulse width changes on the QXI probe
1H pulse width changes on the QXI probe. It has been noticed that the roughly 4 dB LESS
attenuation is required to achieve the same proton 90 degree pulses previously attained on the instrument.
Thus, previously for ubiquitin in 95% H2O, the 90 degree pulse width was approximately 8us at pl1 = -1dB.
Presently, an 8us 90 degree pulse is achieved using pl1 = -5dB. This change in power output seems to
be reasonably uniform over a large range, so as a starting place you can assume that it will take
approximately 4 dB less to achieve the same 1H 90 for ALL 1H pulses. Although many tests and boards
have been replaced to try to diagnose the problem, a solution has not yet been found. Although somewhat
disconcerting, the good thing is that the spectrometer seems to be perfectly functional. Thus, you should
feel confident in continuing to use the instrument as is, but also know that steps are being taken to resolve