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
Wednesday, November 10, 2010
Monday, October 18, 2010
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
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
Monday, October 11, 2010
NMR outages 10/14 & 10/15
FO has decided that there will be several outages over fall break that will affect the access to NMR in Malott.
#1) On Thurday 10/14 Florence (the 400 on the 3rd floor of Malott) will not be available. There will be no lab air from 8 AM to 10 PM and (as all of you know) we use compressed air to get the sample in and out of the magnet. Hence, I will shut down Florence from Thursday morning at 8 AM to Friday morning at 8 AM.
#2) On Friday 10/11 from 1-3 PM there will be a power outage in the new side of Malott. This outage will force me to shut down Paris and Siena (500s in Malott basement) at ~noon on Friday. Furthermore, I will have to warm my cryoprobe starting at ~8 AM. I will get Paris back up and running on Friday afternoon by 4 PM. Siena is a bit more complicated (see below).
#3) We have noticed that our cryoprobe is not behaving as well as it once did. Any troubleshooting will require us to remove the probe from the magnet. Since we have to warm the probe on Friday we will use this time to troubleshoot issues with the cryoprobe. The downside is that we will not be able to cool the probe back down right away. Our tentative plan (assuming that we can fix our problem and not have to send the probe to Bruker for repairs) is to recool the probe on Tuesday 10/19. Hence, the cryoprobe will be available on Wednesday 10/20 at the earliest.
We apologize for the inconvenience,
Justin
#1) On Thurday 10/14 Florence (the 400 on the 3rd floor of Malott) will not be available. There will be no lab air from 8 AM to 10 PM and (as all of you know) we use compressed air to get the sample in and out of the magnet. Hence, I will shut down Florence from Thursday morning at 8 AM to Friday morning at 8 AM.
#2) On Friday 10/11 from 1-3 PM there will be a power outage in the new side of Malott. This outage will force me to shut down Paris and Siena (500s in Malott basement) at ~noon on Friday. Furthermore, I will have to warm my cryoprobe starting at ~8 AM. I will get Paris back up and running on Friday afternoon by 4 PM. Siena is a bit more complicated (see below).
#3) We have noticed that our cryoprobe is not behaving as well as it once did. Any troubleshooting will require us to remove the probe from the magnet. Since we have to warm the probe on Friday we will use this time to troubleshoot issues with the cryoprobe. The downside is that we will not be able to cool the probe back down right away. Our tentative plan (assuming that we can fix our problem and not have to send the probe to Bruker for repairs) is to recool the probe on Tuesday 10/19. Hence, the cryoprobe will be available on Wednesday 10/20 at the earliest.
We apologize for the inconvenience,
Justin
Wednesday, August 25, 2010
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
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
Thursday, July 29, 2010
Website update
I uploaded a bunch of new documents to the website this morning. I wanted to make note of a few of these.
#1) Sarah and I will begin implementing a new training protocol in the fall. See the training page for details. New users will have to study the document "Things to know before operating an NMR spectrometer" and pass a test before training. Then Sarah will walk through how to record a 1D 1H spectrum. She'll create their account but not activate it. Then, when they have a sample, they'll do a follow up training with me.
I'm trying to combine the best aspects of user training that I've observed by looking at NMR facility sites at different universities. Most of our user training procedure comes from Dave Vander Velde - formerly at KU, now at CalTech. I got the "Thing to know ..." idea from Jeff Simpson at MIT. I got the follow-up training idea from Rich Shoemaker - one of my mentors - at CU-Boulder. I got other good ideas many, many other facilities (too many to list).
#2) We're going to add checklists for every open-access instrument. I got this idea from Atul Gawande, a surgeon at Harvard Medical School. I'll add an essay I wrote about the philosophy of checklists tonight or tomorrow. Check our documents page for the checklists and keeps your eyes open for these on the instruments. Hopefully these help us with "avoidable failure".
J
#1) Sarah and I will begin implementing a new training protocol in the fall. See the training page for details. New users will have to study the document "Things to know before operating an NMR spectrometer" and pass a test before training. Then Sarah will walk through how to record a 1D 1H spectrum. She'll create their account but not activate it. Then, when they have a sample, they'll do a follow up training with me.
I'm trying to combine the best aspects of user training that I've observed by looking at NMR facility sites at different universities. Most of our user training procedure comes from Dave Vander Velde - formerly at KU, now at CalTech. I got the "Thing to know ..." idea from Jeff Simpson at MIT. I got the follow-up training idea from Rich Shoemaker - one of my mentors - at CU-Boulder. I got other good ideas many, many other facilities (too many to list).
#2) We're going to add checklists for every open-access instrument. I got this idea from Atul Gawande, a surgeon at Harvard Medical School. I'll add an essay I wrote about the philosophy of checklists tonight or tomorrow. Check our documents page for the checklists and keeps your eyes open for these on the instruments. Hopefully these help us with "avoidable failure".
J
Wednesday, July 28, 2010
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.
#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.
Thursday, July 15, 2010
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
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
Tuesday, July 13, 2010
Swapped Probes in Paris
This morning I swapped the TXI probe in Paris for the BBO. The BBO probe should give better results for 13C-detected experiments such as C13CPD and C13DEPT135. 1H-detected experiments will suffer a bit, though I doubt anyone will be able to tell. The other advantage of the BBO is that it is better suited for VT-NMR and we can do "exotic" nuclei. In fact, I'm going to do some 14N this afternoon.
The BBO is a bit shy of lineshape and 1H and 13C sensitivity specification, but we'll get that worked out, soon. Another important task is to make 3D shimmaps of this probe. With the shimmaps in place, we'll (hopefully) be able to shim the probe up faster after swapping it in.
Justin
The BBO is a bit shy of lineshape and 1H and 13C sensitivity specification, but we'll get that worked out, soon. Another important task is to make 3D shimmaps of this probe. With the shimmaps in place, we'll (hopefully) be able to shim the probe up faster after swapping it in.
Justin
Friday, July 9, 2010
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
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
Thursday, July 8, 2010
Not making lineshape spec of Yosemite
Unfortunately, we can't make lineshape spec on Yosemite (spinning hw = 0.38 hz; hump = 6.1/14 Hz). Fortunately, we are close enough that most users will not even notice. The problem is high-order off-axis shims, which can be tricky to dial in. We'll keep working on it and hopefully soon be able to report that we are making spec or at least that we are getting closer.
Justin
Justin
Wednesday, July 7, 2010
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.
The KU NMR Lab Blog
Over the last couple of months I have been updating the website (http://www.msg.ku.edu/nmr/home.html). One issue that concerns me is communication with our clients. There is a listproc mailing list, but I only like to post highly critical messages to that list. It occurred to me that we needed a less formal way to keep our users abreast of non-critical developments in the lab, including things like
*Continued developments on the website
*New protocol
*Instrument specifications
So I decided to start a blog. Let's see how long this lasts. I'm guessing about a month. Hopefully, I can keep it going a bit longer than that, because this blog may give me a good place to chart the progress of the lab.
Justin
*Continued developments on the website
*New protocol
*Instrument specifications
So I decided to start a blog. Let's see how long this lasts. I'm guessing about a month. Hopefully, I can keep it going a bit longer than that, because this blog may give me a good place to chart the progress of the lab.
Justin
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