Bruker Avance 500 Status Reports
This is a cumulative index of status reports for the Bruker Avance500 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.
9/10/2002, edc, atmm
"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.
atmm tuning curve . I have learned that the problem with the 1H wobble
curve not displaying properly can be avoided by typing "acqu" prior to issuing
the "atmm" command. I have tested this, and indeed it seems to correct the
problem. In general, whether one is using the "wobb" command or the "atmm",
my recommendation is that you enter the acquisition window (by typing "acqu")
prior to issuing the command that initiates the wobble procedure ("wobb" or
9/04/2002, Computer Repaired
Computer repaired. The Avance500 computer has been repaired and
is now operational. Each of the user accounts has been verified - both
to ensure appropriate access privledges and gradshim functionality. The
only unresolved issues at this point include the "edc" bug and the 1H atmm
bug (note the edc bug is now occurring on all three spectrometers).
8/30/2002, Shutdown - Computer Rebuild, New UPS Supply for Host Computer
Shutdown - Computer Rebuild. The Avance500 will be shutdown starting Wed, 9/03/2002.
This will enable rebuilding the SGI host computer which was inadvertantly damaged while
attempting to troubleshoot a software problem. Anticpated downtime is 3 - 4 days.
New UPS Supply for Host Computer. The SGI host computer for the avance500
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 avance500.
7/29/2002, ACB DISPLAY, ATMM
ACB DISPLAY. The ACB display on the bsms keypad is now functioning. The problem
was due to a bad board which was replaced. Note, in addition to the led display on the
bsms keypad, you can also visulize the acb display from the "windows" menu in xwinnnmr.
ATMM. The issue with the 1H atmm procedure has not been resolved.
Most generally what happens is that atmm initiates a wobble curve with a 40 MHz
sweep width (from 480 to 520 MHz), but only the first 10 MHz of this is displayed
(480 to 490 MHz). The problem is that
under these circumstances the curve is not accurately displayed (it is labeled as being centered
about 500.13 MHz with the scale ranging between 495 MHz and 505 MHz).
The solution to this is to click the WOBB-SW button on the left of the screen (after having
typed "atmm" and after having entered the acquisition window by typing "acqu"). Once you have
clicked the WOBB-SW button, accept
the default values. This should then cause the wobble curve and display to reset and properly display
(from 480 to 520 MHz, centered at 500 MHz). Note that even though this is correct, it may still seem "unusual" to you.
The reason for this is that in order for the atmm procedure to work correctly the wobble sw must be
40 MHz. This is somewhat larger than the 10 MHz that has been used in the past when
we tune the 1H channel manually, so you "see" more of the wobble curve.
7/15/2002, AMX2 to Avance SGU Upgrade
Issue. The three channel AMX2 console was replaced with a modern
four channel avance signal generation unit (sgu) console. Additionally, a new
sgi o2 computer, a new shim stack, and two new probes were installed. The new
5 mm txi probe with triple-axis gradients and automatic tuning
5 mm qxi probe with triple-axis gradients.
Some of the details of the transition follow:
Old Data. Only data on the /u, /hinck, and /nall drives from the old
amx500 computer were saved. These data files have been copied over to
the sgi nis cluster:
/u ----> /nmrfac1/amx500_udisk_backup
/hinck -----> /nmrfac1/amx500_hinckdisk_backup
/nall ----> /nall2/amx500_nalldisk_backup
New Computer. The new sgi o2 computer is called avance500.v24.uthscsa.edu.
Access is identical to that of the amx500 computer (that is, access is
restricted to within vlan24). The user accounts have been setup by copying
this information from avance600 - so your username and password should be
the same as what you currently have on the 600. To maintain consistency
with other computer setups in the nis cluster, the data disks are
now named /avance5001 and /avance5002. I have made directories for walker,
olgap, jzuniga, sdeep, and ahinck on /avance5001 and for maria and hardies on
/avance5002. Note that the /avance5001 and /avance5002 disks are read-only
mounted onto the nis cluster with these same names (thus, on instinct for
example you should be able to type cd /avance5001/data/joe_user/nmr and see
your nmr data files). Note also that the /u disk on avance500 is also mounted
read-only onto the nis cluster (as /avance500_u).
Getting Started. After logging into the new system and starting topspin
(version 2.1 is currently running on 500 & 700 and version 1.3 on 600) type "setres" at the topspin
command line. This opens a preferences box. Here I typically chose the
vi editor, ZG safety = off, and the "extended" interface. You should also
go to File --> Search which will open the portfolio editor. Here you should
add the /avance5001 and /avancd5002 disks to your search path. Once you have
done this, go to the file menu and choose save as default (otherwise these
settings will be lost). For your convenience, I have defined an environment
variable that points to the locations of the pulse programs (pp or PP) so
you can type cd $pp (or cd $PP) to change to the location where the pulse
programs are stored.
Hardware Setup. The channels have been setup so as to be consistent with
that used on the 600. 1H is assigned to f1, 13C is assigned to f2, and 15N
is assigned to f3. Unless noted otherwise, all experiments setup under "ref"
are setup use this convention. Note that a rudimentary set of experiments
has already been setup under "ref" on the /avance5001 disk. You should be able
to use these as a starting point for your experiments.
Major Differences. Relative to the amx500, there are many differences
with regard to the hardware available and how to operate the spectrometer. Relativeto the avance600, the number of differences are relatively small. The most important of these is the tuning. Thus, unlike the current 600 setup,
avance500 is equipped with two X-BB preamps. Thus, the current hardware setup
has both the 15N and 13C channels routed through preamps. This means that there
is no need to change the cabling when tuning the 15N channel on the probe. The
other difference is the way in which the tuning is performed when the txi probe
is in place (which is currently the case). This probe is equipped with
an automatic tuning and matching device, which means there are no tuning/matching
rods accessible on the bottom of the probe. To tune using this probe, simply
read in the tuning expt you wish to perform (tune15n.xxx) and then type atmm
(this is instead of wobb; if you have the qxi probe, obviously you type wobb
instead of atmm) which initiates the same type of "wobble" procedure as before.
You can view the wobble curve by going to the acquisition window (acqu). Here
you will not only see the familiar tuning curve, but you will also see a
graphical panel that allows you to adjust the tuning and matching capacitors
for the channel being tuned. The operation of this is more or less self
explanatory (>>> or <<< are course adjustments in the clockwise or counter
clockwise direction while > or < are the fine adjustments). When done, click
file ---> exit on the graphical window, and then return on the lower left of
the topspin main window.
Temperature: I have not yet verified the temperature setting on the txi probe.
Presumably its reasonably close (1-2 degrees at room temperature),
but not perfect. If the exact temperature is
important, you should probably check this using the ethylene glycol sample and
the procedure described on the nmr facility web pages.
Printers: The nmr facility now has its own printer. Its on the lab bench
in the 600 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).
Hardware Configuration Under edasp: The behaviour of the edasp command
has been changed so that users are unable to change connections involving
the preamp. Since most users are not using edasp, this change should
not have any major impact for most users.
Bugs: There are a record number of bugs that I have so far identified! Here
they are - please be patient - I have contacted Bruker about all of these
issues and am trying to work out solutions.
1) The tuning curve sometimes does not display properly when the atmm or wobb
tuning procedure is initiated. There are two potential ways to fix this.
One is to minimize the topspin main window, move the cursor
into the sgi window where topspin was stared, hold down
simultaneously the ctrl and backslash commands (causes topspin
graphics to restart), reopen the topspin main window, and go back into
the acqusition windown (i.e. type "acqu"). The other way is to click on the
button that says wobb-sw (on the left after having initiated wobb or atmm and
after having typed "acqu").
2) The edc command works fine, although it has a bug where it inadvertantly
pops up an error message. The circumstances that causes this is when edc
is used to copy a data set from one user (say "ref") to another (say "ahinck").
Thus, you will find that even though the information is properly entered
(user=ahinck), it pops up an error box indicating that it was unable to write
the new experiment. This is bogus as you will see that topspin is in fact
able to write the data as requested.
3) The LEDs on the top of the bsms keyboard are non-functional (this is called
acb (acquisition control board) display). This is a caused by a
hardware problem. In lieu of this, you can use the graphical
acb display (type "acbdisp" at the topspin command line).