03/12/09

Another reminder: long periods of time are available on all instruments from 9 pm to 8 am, however, if you want to reserve time starting at 9 pm, please do not also reserve time immediately before this as it will be effectively a long reservation starting before the allowed time. The same applies to overnight time ending at 8 am: reserving contigous time starting at 8 am is not nice nor allowed. In other words, if you want to use extended time you have to start 9 pm or after, not before and end at 8 am or before but not after.


01/22/09

It is now possible to login into the Lab computers using your UMich password.


01/16/09

Reminder: According to our Facility rules, NMR time should be reserved AND used by the same person. A user can only use the instruments using his/her own logins: operating an instrument using a friend's account is not permitted. Long periods of time are available after 9 pm or during weekends.


01/16/09

As many of you have noticed, we have been working on a software update on the Mercury 300. Both the operating system and Vnmrj will be upgraded. We hope the new software will be available today. The same upgrade will be performed on the other instruments and workstations during the next few days/weeks. Each computer in turn will be intermitently unavailable during this period of time. After the update, the new version of Vnmrj in the old spectrometers will be more consistent with that in the new spectromenters (Co and Ga) and the operating system (Linux) will have some new features and be easier to use.


08/06/08

The default probe of Cobalt is back from Varian. All nuclei and experiments are possible again.


06/27/08

The default probe and tunning unit of Cobalt have been sent to Varian for upgrade and testing. The spare 400 probe has been installed. Therefore, only H1, F19, C13, P31 and 2H are possible at this time.


06/13/08

The multinuclear probe on Cobalt has (finally!) been repaired.


05/30/08

The Pulsed Field Gradient Unit on the Inova 500 has been repaired.


05/29/08

The Pulsed Field Gradient Unit on the Inova 500 is broken again. Until further notice, nothing that uses gradients will work, including gradient shimming, gcosy, ghmqc, ghsqc, noesy, noesy1D, etc.


05/12/08

An old 400 MHz probe has been installed on Cobalt. Although the sensitivity is not as good as that of the autotunable probe, it is not too different to the Inova's 400. Like the Inova 400, it can do only H1, F19, C13 and P31.


05/12/08

Gallium's styrofoam bucket is now dead. Please use the bucket from the Inova 400 or 500 if low temperature is needed. A replacement will be ordered.


05/12/08

Gallium's white styrofoam bucket, used for low temperature experiments, dissapeared from the Lab during the weekend. If you have it please return it inmediately; if you know who has it or what happened to it please let us know asap. These accesories should not be taken from the Lab since any user can need them at any time.


05/09/08

Cobalt is out of service for the weekend. Its probe has been shipped for repairs. An old probe from the Inova 400 has been installed and will be calibrated on Monday to be used as interim.


05/07/08

The probe on Cobalt is broken. For the time being it can be used for proton acquisitions only (1D proton, cosy, noesy and noesy2D). It will have to be sent to Varian for repairs tomorrow.


05/05/08

The Inova 500 has been repaired. All experiments should function properly.


04/15/08

Our annual license of MestreNova 5.2.1 has been renewed. It is installed and working in one of the workstations in the lab.


04/07/08

It appears that the Inova 500 has developed a new problem. At this time only simple 1D experiments will work (noesy1d probably won't work either).


03/26/08

The Pulsed Field Gradient unit on the Inova 500 is finally back from Varian's repair shop! All 2D experiments and gradient shimming should be back to normal.


03/18/08

Parameters for the following nuclei have been configured in Cobalt: 119Sn, 11B, 51V, 195Pt, 199Hg and 2H. More nuclei can be configured on request. Parameters for 2H and 11B have also been configured in Gallium. To run these nuclei, just select them from the Experiments menu and tune the probe ("Tools -> Probe Tunning -> Tune Probe).

The macro "gradshim" is now working fine for those who want to shim non-deuterated solvents.


03/11/08

Gallium is now open for business.

It appears that Cobalt's magnet is not as stable as the other magnets in our lab (but is still within specifications). This means that the value of Z0 is slowly but continously changing; and over a period of just a few days, the value of Z0 that our macro 'setlock' has stored is so far off that the lock won't engage. If this happens, just click on "Find Z0"; it works quite well. Gallium doesn't have this problem.

03/05/08

Our two new 400 MHz NMR spectrometers, Cobalt and Gallium, are finally installed!! Although they look alike they have different capabilities. Check the Instruments page for details.

Cobalt has a "Dual Broadband" probe similar to that installed in our Inova 400. It has very good sensitivity for C13 and other heteronuclei; better than our Inova 400 and almost as good as our Inova 500 with the switchable probe. It can also measure other common nuclei like F19, P31, B11, N15, Cd113 and Pt195 with automatic probe tunning. It doesn't have a low temperature accessory but can regulate the temperature between ambient and +130 degrees.

Gallium has an indirect detection probe, similar to the one installed by default on our Inova 500. It has excellent sensitivity for proton (higher than that for the id probe in the Inova 500) and is therefore optimum for all experiments that detect protons, like COSY, HMQC, HSQC, TOCSY, HMBC, CIGAR, NOESY, NOESY1D, ROESY, etc. But it cannot detect F19 and the sensitivity for C13 and other nuclei is reduced. It is equipped with a low temperature accessory that allows it to regulate the temperature to between -80 and +130 degrees.

Slightly different software interface. The new spectrometers are running Vnmrj 2.2C. The user interface is a bit different than on the Inovas or on the Mercury 300 but only enough to require a few minutes of getting used to. Furthermore, the Chempack add-on has been added and enabled by default. This package adds more experiments and a few niece extra features. To run a simple spectrum, insert the sample, select the experiment and solvent and lock and shim as usual or click on "Find z0" and "Gradient Autoshim". Finally click on the green "Acquire" button. It is important to notice that now typing go or ga in the command line is not exactly the same as clicking on the Acquire button. The most important difference is that the Acquire button will tune the probe when needed, but go or ga will not. For example, if the previous user run a Phosphorus spectrum and what you want is a carbon spectrum, the probe will not be tuned to C13 and you will only get noise. And since you usually won't know what the previous user was doing, this means that you ALWAYS have to tune the probe to your sample before acquisition. The Acquire button should take care of that, but you can also tune it on demand by clicking on "Tools ->Probe Tunning -> Tune Probe" and then clicking the nucleus of your choice. Another nice feature of Chempack is the capability to create and run "experiment queues". These are lists of experiments to be performed in sequence on the same sample. To set up a queue, click on the "New Sample Q" button on the lower left corner of the vnmrj window and then click on the experiment buttons that you want, for example Proton, Carbon, gCOSY and gHSQC. You will see the individual and total acquisition times and you can even change the default parameters, like the number of transients, by double clicking on the list names. Enter a name on the "Sample name" field and click on the green "Submit" button to start the acquisition. The spectra will be saved in your vnmrsys/data directory with the name you provided.

Temporary usage policies. Tentatively, users will be allowed up to 3 hours of instrument time during weekday hours (8 am to 8 pm). After that time and during weekends, there is no time restriction. This policy will be under observation and will be reviewed in the next few days. Final policies regarding the new and old instruments will be published here after the trial period.

Cobalt is now open to be used, but it will probably be a good a idea if you use it for the first time when we are in the lab so we can help you if you have problems or questions. Gallium will be open to the public in a day or two. Most of our custom macros have been ported and installed, but there are a few that require some work and testing. They will be installed soon.

Please, please, please, be careful with your samples. Avoid breaking your nmr tubes either over the working desk or on the magnet. Lets try to keep the instruments new and clean for the longest time possible.


12/20/07 Due to the expected decrease in instrument demand over the holiday break, and to give users better access to the instruments, the normal rules will be changed as follows.
Please be considerate to other users and do not make a long reservation immediately after a previous long reservation. "Long reservations" are reservations of more than 1 hour. This will give users who only need a few minutes the opportunity to run their spectra at several times during the day. For example, if someone has already reserved the instrument from 9am to 12pm and your experiment requires 3 hours, allow at least an hour for other users to run their short spectra by starting your reservation after 1 pm.

12/20/07 The Mercury 300 has a new place in the lab and is now ready for use!









11/29/07 The Bruker AMX 500 has been decommisioned and will be replaced by two new Varian MR400 spectrometers. Installation is expected in January.

6/21/07 A common problem that occurs when plotting 2D spectra with high resolution 1D "projections" is that the intensity of the signals of interest in the projections is very weak as illustrated in the next figure.

 


This happens because the macros plcosy and plhxcor use the tallest peak in the displayed region to determine the "optimum" intensity. If that region contains one or more very tall peaks like methyl groups or solvent residues, the remaining signals will appear very weak. Unfortunately, Vnmrj does not have an easy mechanism to set the 1D intensities manually.

To reduce this problem, our custon macros UMplcosy and UMplhxcor were modified. When you use these macros and indicate the location of a high resolution spectrum (for example, the command UMplcosy(5, 1.5, 1) indicates that the high resolution proton spectrum is in experiment1) the macros use the current vertical scale (vs) of the high resolution spectrum and attempt to plot it on the top or side of the 2D at approximately the same intensity. Before using these macros, setup your high resolution spectra, for example in experiments 1 and 2 and display them on the screen at the intensity that you want to use for your projections. Then go to the experiment where your 2D spectrum is located and type the appropriate plot command. Finally, remember that these macros require a page or UMmailpage command to send the plot to the printer or to an email box. 5/3/07 A Frequently Asked Questions list has been added to the Documentation section. Inside it you can find information about importing spectra into Microsoft Office documents, file transfers, creating plots with insets, baseline corrections, accurate integrations, and some other short topics. Check this document regularly as it is going to be growing and changing frequently.

5/2/07 One of the Linux workstations in the NMR lab has been switched to Microsoft Windows and in it we have installed Microsoft Office, ChemOffice and the latest version of the NMR processing software MestReC now called MestReNova. This program is easy to use and produces very nice looking 1D and 2D spectra. It is easy to annotate the spectra and to paste chemical structures from ChemDraw. The spectra can then be copied and pasted into Word or PowerPoint documents. It provides a very good alternative to Vnmrj for processing and plotting of spectra. Your files on the spectrometers can be easily accessed through network drives (X:\, Y:\ and Z:\) on this computer; you do not need to transfer them first with sftp.

Notice however that spectra inserted in this way can be very large since you are inserting the actual NMR data and not just an image. The advantage is that you can double click the embedded spectrum and change anything you want, but if you have many spectra in your document its size can become quite large. Give it a try.

4/12/07 To import spectra into Microsoft Word or PowerPoint, Vnmrj provides only one option; "plot" the spectrum to a file. The resulting file is in postscript, a vectorial description of the file, and Word or PowerPoint can easily import it if it has the file name extension .eps (for encapsulated postscript). You can simply drag the file's icon into the the Word document and drop it in the desired location. After that, you will probably have to change its size and other properties. The spectrum will look great when printed, but unfortunately it won't look that great on the computer's display (or on the projection screen). You will also have to transfer your postscript files, via sftp or with a flash drive, to your Windows computer. To help with these issues a new macro, UMmailpage
, was developed. This macro was designed to be used as the page macro, i.e. first you build your plot with plotting macros like "pl pscale" and then you type UMmailpage. The macro will save the postscript file, convert it to a png (portable network graphics) file and send both files via email to you. The png file is a bitmap file similar to the most common jpg format but with some additional advantages and can be imported into Microsoft documents in a similar fashion by dragging and dropping. The png file is created in high resolution and will look well both printed and displayed. It can be edited with a graphics program like Photoshop to insert legends or chemical structures.

When executed, UMmailpage will ask you for a file name, your email address and a line width for the plot. The default line width, 1 pixel, produces very thin lines which may be difficult to see from the distance or when the plot is reduced in size. For presentations, a line width of 2 or 3 is recommended.

4/6/07 A new, more detailed application note about Kinetics experiments with Vnmrj is now available in the Documentation section. New macros to perform baseline correction and integration along all spectra in an array were developed and are explained in the hand out.
12/20/06 The spinner's turbine of the Inova 400 was removed from the magnet and throughly cleaned. The intermittent spinning problems experienced in the last few days should now be gone.

12/22/06 Due to the low demand of the instruments during the Christmas break, the maximum time allowed during prime time has been increased to 3 hours per instrument. The normal limit of 50 minutes will be restored in January 2nd. Enjoy!

11/21/06    As we all know, problems occur more often than we wish during the operation of the spectrometers. Problems include samples not spinning, computer hangups, spectrometer malfunctions, software bugs, etc. To facilitate the correction of common problems, a page has been posted in this web site and a link was created in Vnmrj's Help menu in the lab's computers. This way, when a problem arises you can view its solution directly in the spectrometer's computer. No longer will you have to search for the "white binder" in the lab. In the Help menu you will also find a link to the Scheduler and to the Application Notes (HowTos) prepared in the Lab.


11/17/06 A new application note about Noesy 1D spectra with Vnmrj is now available.

11/09/06 Finally! The switchable probe (sw) of the Inova 500 is back from repairs.

10/17/06 The indirect detection probe (id) for the Inova 500 is back. The probe was calibrated, tested and all experiments appear to be working fine. The switchable probe (sw) was sent for repairs.

9/29/06 A new application note about kinetics experiments with vnmrj is now available.

9/25/06 In order to help users with very limited amounts of sample, we have acquired a few Shigemi NMR tubes. These tubes are made of glass with magnetic susceptibilities matching those of the most common solvents and allow the use of smaller sample volumes. The solution is confined to a region inside the probe's measuring coil, thus increasing the sensitivity. Compared to a regular tube, the overall acquisition time is reduced by a factor of about two. We have tubes for CDCl3, CD3OD, D2O and DMSO-d6. You can borrow these tubes for testing or occasional use but we encourage research groups to buy their own if they frequently have low quantities of samples.

10/17/06 The VnmrJ software in the Inova 400 was upgraded to version 2.1B. All experiments are operational.

10/17/06 The VnmrJ software was upgraded from version 1.1D to version 2.1B on all computers in the lab except the Inova 400 and the Mercury 300. The Inova 400 will be upgraded sometime this week. The Mercury 300 will continue with the current version until Varian releases an update compatible with Mercury consoles.

9/25/06 The plague fell upon the 500!. The heteronuclear channel on the sw probe has developed a problem and is unable to pulse. The probe will probably have to be sent for repairs after we get the id probe back from Varian which will likely happen early next week. In the mean time, unfortunately it won't be possible to run experiments involving any nucleus other than hydrogen. That includes 1D and 2D experiments like HMQC or HSQC. All proton-only acquisitions including NOESYs or COSYs are OK.

9/25/06 The purpose of the news presented in this page is to keep you informed of very important information regarding the operation of the spectrometers and the lab. It is not useless technical mumbo jumbo but information that can actually help you and all users in the lab. For example, a user recently changed the "probe" parameter in the Inova 500 to the -currently incorrect- value "id". The result was that for a couple of days ALL users had hard time shimming and two-dimensional spectra were very noisy (The attributes of the parameter are now different, so no user can modify it anymore). Had he bothered reading this page he would have known that the id probe was sent for repairs.
Reading the news is not only encouraged but required to use the Facility. Please make a habit of checking for new news before you blindly click the next link.

9/15/06 An updated guide to run two-dimensional experiments with VnmrJ is now available.

9/12/06 A ghost broke a sample in the lab this morning. The sample apparently contained acetic acid and who knows what else. When the next user came and inserted her sample in the spinner, she noticed the odor and realized that the outside of the tube was covered with residues of the spilled solution. This, of course, is very unfriendly to say the least. The acetic acid or whatever that was left in the spinner caused the o-ring in the spinner to expand, making it useless to keep tubes in position. The inside of the spinner had to be cleaned and the o-ring replaced. It is very irresponsible to break samples and just walk away without doing a thorough clean up and notifying us. Potentially the next user might absorb a toxic, unknown chemical through the skin. The inside of the magnet and the probe can also get contaminated. Residues of chemicals will accumulate in the magnet until samples no longer spin properly. In other words, it will affect all users of the lab. Please let us know when a sample is broken, even if it is outside the magnet so we can make sure that everything is properly cleaned. And please notify us when you notice that some other, unfriendly user breaks a sample but does not tell us. Negligent users will have their privileges revoked.

9/11/06 The Inova 500 now has the switchable probe installed and tuned to proton and carbon. Note that the sensitivity for both nuclei, and especially for carbon, is better than in the Inova 400. See the Instruments section for actual signal to noise figures.

9/06/06 We have determined that the default probe on the Inova 500 is responsible for the problems described below. Therefore, the indirect detection probe ("id") will be sent for repairs on Monday 11. It will take about a month to have it back. During that time, the switchable probe ("sw") will be used. Although this probe is capable to perform all the experiments the id probe can perform, its sensitivity is noticeably lower. Please plan your experiments accordingly.

9/06/06 A problem was detected on the Mercury 300. The problem appears only on proton spectra as a bunch of glitches near the center of the spectrum. Other nuclei are fine. We are currently working to pin point the source and fix it.

8/23/06 A problem was detected on the Inova 500. The problem appears on heteronuclear correlations acquired with C13 decoupling like Ghsqc, Ghmqc and hmbc. When broadband decoupling is on, power glitches appear in the FIDs that severely increase the noise in the 2D spectrum and introduce other artifacts. We are currently working on a solution to this problem. In the mean time, to minimize the effects, the power used for decoupling has been decreased but at this power level decoupling is not completely effective and residues of the undecoupled signals can be seen in the spectrum. However, homonuclear correlations (COSY, noesy) and 1D experiments like H1, noesy1D and C13 are working correctly.

8/29/06 When plotting a heteronuclear 2D spectrum, e.g. a hsqc, it is desirable to plot high resolution spectra along its sides. The macro to do this is plhxcor(). For this macro to work correctly as supplied by Varian, all spectra must have been acquired on the same spectrometer, otherwise the chemical shifts won't match. This makes sense as a 1D spectrum measured at a different field may look different. It will certainly be the case for proton spectra because their splitting patterns are so sensitive to field strength. In our lab this is inconvenient as the most sensitive spectrometer configuration for C13 is the Inova 400 while the most sensitive (and recommended) for heteronuclear 2D correlations is the Inova 500. To provide more flexibility, the macro plhxcor has been modified so that it is now possible to plot a C13 spectrum collected on the Inova 400 along a 2D collected on the Inova 500. Keep in mind that this is not formally correct as you are displaying and comparing spectra at two different fields. However, in the case of natural abundance C13 spectra and other nuclei lacking homonuclear coupling, and for appearance purposes, it may be acceptable.

8/24/06 Last Monday, we found that the probe on the Inova 500 was mistuned. Yesterday, the temperature controller on the Inova 400 was off and today, we found that the gradients unit on this same instrumen had been turned off. Most 2D and other experiments will fail without the gradients unit or without a properly tuned probe. Needless to say, this produces a lot of wasted time by all other users (and us) and general agravation. We remind you that nobody is authorized to make changes of any kind to the instruments, except for changing the 1/4 wavelength cable on the Inova 400 and Mercury 300. Those who don't follow this rule will have their use privileges suspended!

6/28/06. We found the probe on the Inova 400 mistuned. This probe is more difficult to tune than others because each coil has to be tuned to two nuclei (1H/19F and 13C/31P) simultaneously. Please don't attempt to tune this or any other probe yourself. Contact us if you suspect a probe might be miscalibrated. The probe was retuned and pulse calibrations were perfomed.

6/22/06. Please, please don't drop the spinners. They may become unbalanced and produce severe glitches, similar to spinning side bands but worse. They are expensive to replace too. Recently, we have had to replace a few of them due to user abuse.

6/21/06. The Frequency Synthesizer in the Inova 500 was replaced and all pulses were recalibrated. Last week, the digitizer board was also replaced. These changes should fix all the problems that have appeared in the last few months. All pulse programs should work correctly now.

6/06. We are currently testing an update to Vnmrj, version 2.1B. This one has an improved graphical interface and some bug corrections. It will be first installed in the Inova 500 and later in the Inova 400 and all data stations in the lab. This version is incompatible with the Mercury 300 for now; a new compatible version is expected in the future.

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