Now witness the firepower of this fully ARMED and OPERATIONAL NMR Spectrometer.

Now witness the firepower of this fully ARMED and OPERATIONAL NMR Spectrometer!

I wanted to thank everyone for their patience over the past few weeks while I tinkered with BigSur. This afternoon I put the BBO probe back into the instrument and recalibrated it. With this probe everyone should enjoy higher signal-to-noise on carbon-detected experiments like the 1D 13C, DEPT and APT (although I would be remiss in my duties if I didn't point out that Siena is more than 4x more sensitive than BigSur!)

The reason I had to perturb BigSur was a) replace the workstation; b) diagnose some unsettling problems with 1H sensitivity. The computer was swapped last month. Switching the probes help diagnose a problem with our receiver preamplifier that was introducing extra noise into 1H spectra. Although this noise was minor and I'm certain that no one noticed, we could see it in our standard tests and Sarah and I don't like it when our spectrometers misbehave!

As always let us know if you have any questions,

Justin

Care and Feeding of BigSur

Today is maintenance day on BigSur, the CMLD-SCC NMR. I made two major upgrades:

#1) BigSur has a new workstation. I swapped the old workstation (which had a bad fan) for a brand new computer. As far as I can discern the configurations are the same, however let me know if you notice any odd behavior. The only difference you should be aware of is that you'll need to remap your network drives in order to access your data remotely. I synced the data with the old computer, so if you remap the drive you should be able to continue as if nothing changed.

#2) I swapped the probe. The old (BBO) probe could not be tuned properly on the 1H channel, leading to large(r) pulse widths, low(er) 1H signal-to-noise and less 1H decoupling bandwidth. I put a different probe (called a BBI) in the magnet. This probe will have slightly better 1H sensitivity at the cost of less 13C sensitivity. Hence, I would recommend considering sending any 13C-detected experiments to the cryoprobe via our courier service.

Justin

Lab cleaning

Recently, I cleaned the lab in SBC. This task included sweeping all the sand and salt off the floors, dusting the countertops, organizing the bookshelves and properly discarding of some abandonded samples.

Please try to keep the lab clean and orderly. And pick up NMR tubes. Refer to NMR lab chemical hygeine plan (http://www.msg.ku.edu/nmr/Documents/ChemicalHygiene.pdf) for details.

Thanks,

Justin

Instruments on West Campus Down for 1.5 hours

Due to air compressor maintenance, the NMRs in SBC will be down from noon to 1:30 PM on Wednesday 2/9/11. We apologize for any inconvenience.

Justin

1H pulse width recalibrated on BigSur

We got a report that a DEPT135 spectrum did not look good. I confirmed this observation using my favorite sample, 3-heptanone in CDCl3. When a DEPT looks bad it is usually incorrect pulse widths. Sarah recalibrated 1H and 13C pulse widths and now the DEPT looks great. Yeah Sarah!

One problem - why is the 1H pulse width so far off? The probe tuning is and and we cannot tune the 1H channel properly. It seems that at some point we have fried the probe and will have to send it away for repair. It will be a major priority to discover how we did this damage!

J

Cleaned Shimstack on BigSur

Recently, the ICON-NMR queue on BigSur has been failing more often than usual. Sarah traced these errors to spinning problems. She tried our usual methods (recalibrating spins) to solve this problem. However, error messages still disrupt the queue. This afternoon, I took more drastic measures. I removed the probe to check for a cracked insert. The quartz insert was fine. Then, with help from Nadia of the APL lab I removed the shimstack.

HOLY COW. It was the most gunked up shimstack I have ever see. I'm shocked samples would spin at all. I cleaned the shimstack and reinserted into the magnet. After a 3D topshim (presumably necessary because I didn't get the shimstack back into the magnet at the same angle I took it out) I tested the shims on the lineshape sample. My results are 0.28; 3.5/10.9, just missing spec. But close enough to use.

Justin

BigSur2

On Monday afternoon I noticed that the CPU fan was not working on the workstation to bigsur. Obviously, this failure is related to fan problems we noticed earlier. I'm not sure if lubricating the fans prolonged or decreased their lifetime. Whatever the case, this hardware failure forced me to stop procrastinating and swap the PCs.

On Tuesday morning I had to take BigSur offline to configure the new computer. I had a humorous and embarrassing call to IT that I should relate for posterity. I had the computer properly networked then I installed Topspin 2.1 and the computer wasn't pulling the right IP address and hence, not getting on KU's network. You'd think after years of graduate school I could follow a simple cause-and-effect. Topspin statically sets the IP of your nic so that you can communicate with the spectrometer, properly. Unfortunately, I registered that nic in Proteaus (technically I didn't register anything in Proteaus because I don't have access. My colleague Jim Knoop register it for me) before the TS install. So I had to set that nic back to pulling dynamic IP. I think I set the other nic to talk with the console. If I can't get the console to communicate the network configuration will be the first thing I check.

At any rate, I set up the network, reset the exports to share drives, reset the mount points on all of the processing stations in SBC, set up samba and I think I'm ready to go.

Except, I don't have the license file from Bruker. I hope they get that to me soon, because I'm frying the processor of the old workstation every second I run it. Let's hope it survives.

Justin

update on BigSur workstation upgrade

We've had some issue with upgrading the workstation for BigSur. I don't want this to turn into a whiny blog, so I'll try to stick to the facts.

#1) I was impressed with the feature of Topspin 3.0 when I saw the demo at the ENC and I thought that this software would be very convenient for users of BigSur. When faced with the need to upgrade the workstation, I saw an opportunity to expand our capabilities.

#2) Topspin 3.0 requires a 64-bit computer and CentOS linux. We purchased a nice Dell Precision T3500 64-bit workstation and I installed CentOS. I'd configure the workstation and was ready to install Topspin 3.0 and connect to the spectrometer.

#3) Then my good friend Asokan mentioned that he didn't think Topspin 3.0 would work with older consoles. Older consoles - I thought maybe it wouldn't work with DRXs, but BigSur is an AV, purchased in 2004. Turns out he was right. Topspin 3.0 requires hardware that BigSur does not have (a digital receiver unit rather than a RX22 receiver). Hence, even though this console is only 6 years old, it is not eligible for the latest software. NMR technology is advancing rapidly!

I'm a bit frustrated because I told my sales rep my BH number before placing the order for TS3. Clearly, I should have asked more questions, but it doesn't seem too much to ask for Bruker to not sell me things I don't need. Lot of negatives in that last sentence - sorry.

#4) I reinstalled RHEL4 and am configuring the workstation. Strange issues with this too, because the NIC on the motherboard isn't compatible with my kernel.

http://www.linuxcompatible.org/RHSA-20100394-01_Important_kernel_security_bug_fix_and_enhancement_update_p144094.html

Fortunately I have another NIC, but I get to go through the fun of setting up one NIC in Proteaus to upgrade the kernel, then reset Proteaus with the second nic.

#5) We're still waiting for license for TS2.1.

Hope that wasn't too whiny. Cowboy up.

BigSur Workstation

This afternoon I shutdown the workstation for BigSur. Sarah had noticed that the computer was making an horrible sound and I wanted to troubleshoot it. The CPU fan was the culprit. Since fans are cheap, it would make sense to replace it, however, the fan is a very unusual size (65mm x 65mm x 10mm). I scoured the internet and went to three different stores in town and couldn't find anything!

Because of the high demand from the CMLD and SCC, I didn't feel like I could keep this spectrometer down. The fan seems to be functioning properly, so I decided to reattach the workstation to the spectrometer, even with the noise. Then I read that you can fix a noisy fan with a few drops of oil (http://www.zdnet.co.uk/news/processors/2003/06/03/fix-noisy-computer-fans-with-a-drop-of-oil-2135514/). I was skeptical, but also desperate. Maybe it is wishful thinking on my part, but it seems a bit quieter. Tom Coombs said it sounds like trickle of water. Think of the NMR lab as your zen rock garden and come to mediate to the soothing sounds of a gentle mountain stream.

This issue does add some urgency to updating the workstation for BigSur.

Justin

BACs on BigSur back up

Last night the BACs autosampler failed to run the queued samples. This is the 2nd night in a row that the BACs failed. I'm not sure what caused these failures or if they are related. My hypothesis is that someone interfered with the BACs while it was in motion loading or unloading a sample. I have observed that this confuses the software and stops the automation.

I sent an email to all bigsur users and put a sign on the BACs reminding people not to interfere with it when it is in motion.

Justin

Lineshape on BigSur

While troubleshooting another issue, I'll see if I can shim to lineshape spec on BigSur. For non-spinning I get hw = 0.42 Hz and hump = 6.1/11.3 Hz, which is close enough to spec, that I'm thrilled. In fact, these are the best non-spinning results we have recorded since we began keeping records in October 2009. For spinning, I get hw = 0.35 Hz and hump = 3.3/8 Hz, which makes spec. I like these shims so much, that I update the shim file.