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 “atmm”)

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 probes are:

5 mm txi probe with triple-axis gradients and automatic tuning and matching

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 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 ( 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).