Biomolecular NMR Facility
A Data Processing computer is available in the lab. Data can be transfered from Spectrometer computers to this computer for further processing and viewing in TopSpin. This computer also has its own IP address to facilitate data transfer to another computer. Details of operation are posted next to it.
Field Cycler (FC) on NMR600
Field Cycler Users
Field Cycler related errors
Please choose IconNMR from the left side panel for details
Put samples with spinner in the carousel sampleholder, and record the corresponding positions of all samples.
Inject the first sample, lock, shim, tune and match the sample, and run a pulsecal to estimate the P1 of the first sample.
In TopSpin, type "iconnmr" or "icon" to open IconNMR interface.
Select "IconNMR Automation", then select user.
Select "IconNMR Automation", then select user.
Double click the holder number which has your first sample.
Change/edit the following information if necessary(1) Disk and Name:
To the login account NASA, and we name the experiment set by the date, for example 01052020
(2) Experiment number: Check the data folder first. You may set any number but make sure it won't overwirte any existing important data..
(3) Solvent: it should be the deteurated solvent in the sample.
(4 )Experiment: Please read carefully the description of the experiment to make correct selection.
(5) Priority: not necessary to set it if you submit the experiment in your desired order.
(a) Acquiision parameters. You may click on icon to edit a set of specified parameters. Or go to the top menu bar and select /parameters/Edit all acquisition paramenters, which is open the AcquPars window in topspin. After editing, you can click on Return to IconNMR to go back to Automation window.
Note that you should set temperature here (TE). When IconNMR automation starts, a window will pop up asking you whether you want temperature be regulated. If one temperature will be used for all samples/experiments, make sure set that temperature to all entries.
(b) Locking, Shimming options. You may change the settings by clicking on . I recommend NOT to tune and match X-channels, if you will adjust it before starting the automation.
(9) Click on “Add” to add more experiments to this specific sample. Right click the experiment, you may also see "Iterate" option, which allow you to copy the same experiment including customized parameters.
The “Copy” option allows you to copy the already set-up experiment to the next holder number/sample, and then edit only what is necessary. Repeat this step to cover all the holder numbers that have samples. Use "Delete" option to remove entries that have no samples.
Review all the experiments that have been set up. Highlight the holder number, then click “Edit” will allow you to modify that experiment.
Highlight the holder number then click on “Submit” to add the experiment to the queue one by one. You may highlight multiple holder numbers at once.
Click “Start” to run the queued experiments. You may still any experiment that has not been running yet.
At the end, you must quit the automation mode by clicking on the stop icon “” . After that, you can set up single experiments in TopSpin window, which is the "manual mode". Note that there may be a bug in the iconnmr and you won't be able to quit/close iconnmr window or TopSpin, and you have to log out from your account to terminate the program.
By default, the 2D experiments in iconNMR will create and run a 1D proton experiment to be used as a reference to SW optimization. You may choose an existing good 1D instead, or set ns in the 1D experiment properly so all signals of interests will have reasonable/good intensities. Alternatively, an normal/N version (opposite to the composite/C) of any 2D experiments can be created for 1H SW manual adjustment in iconNMR.
1. Open Filezilla, go to File/Site manager, and create an New Site for frequent use.
2. In Filezilla main window, click on the icon "open the site manager", and choose the remote computer you want to access.
3. If all the information in the site-manager was correct, you should be able to see files from the remote computer.
4. To transfer files, go to the desired file directory on both local and remote sites and copy the files.
Note that you may not have the write permission on the remote site.
Possible Filzezilla related issue
Problem: NMR Spectrum does not show correctly in TopSpin after the data was transferred by FilleZilla
Cause: The ser file may have been altered during transfer. If so, in the desination folder you will see a different size ser file.
Solution: Go to FileZilla Client menu, Edit/Settings/Transfers/File Types, change Default Transfer Type to "Binary", and uncheck Treat files without extension as SCII file. Then re-transfer the data.
You may use the following procedure to validate the setting temperature, ranging from 282K-330K. Temperature correction is routinely checked by the facility Note that temperature correction is usually being enabled which should not be altered by users.
CP800 NMR Spectrometer is equipped with a special CPQCI probe which can run high temperature experiments. To set up a high temperature experiments, you need to know the followings:
The CPQCI probe has operating temperature range from 5 °C-135 °C.
Use a ceramic spinner for experimental temperature higher than 50 °C / 323 K.
To run a low temperature experiment, such as at 5 °C, you may need to set BCU / Chiller power to MAXIMUM in temperature control window.
Data Acquisition, Run 'nusPGSv3' for better data point sampling!
- In TopSpin AcquPars window, change the FnTYPE to be 'non-uniform_sampling'. You don’t need to set anything in the NUS parameters block.
- Type 'nusPGSv3' to create a data sampling schedule. Several questions will be asked along the way.
- Random Seed
- - 0 is default and probably what you want.
- - 0 implies the random seed used for random number generation will be selected by the computer.
- - Any other number here means you will also get the same sequence. So lets say you want to compare two acquisitions but are not interested in the differences that might result from sampling differently.
- Sine portion for sampling
- - 2 is default and probably what you want.
- - This is not the place to describe what this means. 2 will result in more points towards the front of the schedule and this is probably best for you. 1 and 0 are experimental and we don't suggest you use them unless you know why you want to.
- Number of points to collect (complex points)
- - When set 128 out of 1280, it is 10% sampling amount. 10% of the current numbers of linear, complex points is selected by default.
- - When running a 2D experiment, you probably want this to be more like 25%. 10% of all the complex points should work for a 3D experiment. 1-2% should work for a 4D. Note that the number you put in here is the total number of points to be sampled, not the percentage.
- Tolerance (as a percentage).
- - 0.01 % is the default. This means the generator must generate the number of points requested above +/- 0.01%. Most likely this means it will generate exactly the number you asked. Sometimes it is hard for the scheduler to find the exact number of samples you ask for so you may need to add some tolerance here. Try changing it to 10%.
- Shuffle the schedule (0 = no, 1 = yes)
- - Default is 0 which means the schedule will be generated with the left most column being "fast" and the right most column being the slowest. I suggest this for starting out.
- - Select 1 will shuffle the schedule. It is perfectly fine to do this as the reconstruction processing will reorder everything in the end anyway. However, note that the first point, (0 or 0,0 or 0,0,0) will always remain at the top.
- - At the end there should be a message” Poisson gas sampling schedule setup finished.”. A nusPGS_setup.out file will be generated into the data directory.
Collect data with the 'zg' command. The schedule used will be deposited into the data directory with the name 'nuslist'. You can use this schedule as is during reconstruction with hmsIST.
NUS data processing
To process the spectrum, go to ProcPars page, and at NUS section, set MDD_mod to either cs or mdd (cs may give better result).
- 2D data processing (TopSpin 3.6 and above, does not require a NUS license)
- Type 'efp' and phase the 1D spectrum. Most likely only PHC0 needs to be adjusted.
- Copy the phasing parameter of the 1D (PHC0) to the 2D. You may or may not need to add 90 degree to the PHC0 depending on the experiment type. Trial and error!
- 2D HSQC: PHC0 in 2D = PHC0 in 1D +90
- 2D TOCSY: PHC0 in 2D = PHC0 in 1D
Phase the 2D spectrum using 'xfb' command 3D data processing
- nmrPipe methods. https://www.ibbr.umd.edu/nmrpipe/nus.html, or http://gwagner.med.harvard.edu/intranet/hmsIST/234Proc.html.
- TopSpin method (Requires a TopSpin NUS license)
The workflow is to extract a 2D plane from the NUS 3D data, and then extract the first row 1D from the 2D plane. Phase the 1D spectrum and obtain its phase parameters. Apply the phase parameters to 2D and adjust PHC0 if necessary to obtain a good 2D spectrum. After that copy the 2D phase parameters to the 3D data, and process the 3D data.
- Open the 3D NUS data set, type 'rser2D' to “Extract a raw plane”. By default a new 2D data set will be generated as expt # 999.
- At the 2D data set, expt# 999, type 'efp' to process the first FID, which has the process number 999 set by default.
- Phase the 1D spectrum, and record its phase parameters, PHC0 in particular.
- Copy the 1D phase parameter(s) to the 2D data set, add 90 to the PHC0 (which is needed in processing a 3D HNCO NUS experiment), and then type 'xfb' to process the 2D data. Signals in the 2D should have the correct phase. If not, removed the added 90 in PHCO and process again. The 2D plane will give you an idea how well the NUS data was acquired.
- Copy the 2D phase parameters to the 3D data set, and process 3D using the command 'ftnd'. “0” should be the option in the pop-up window.
- The 3D data processing may take a few minutes to finish, while its progress is shown at the left bottom corner of the TopSpin window. After it is done, to view 2D planes of the 3D spectrum, use the + , -, or the two way vertical arrow button to move the 2D plane.
For a mixture of two deuterated solvents, you will need to decide which solvent to be locked on, or create a new solvent in the solvent table. Locking on wrong solvent will result in wrong chemical shift measurements.
First of all, make sure you have a required volume of sample with sufficient amount of deuterated solvent. If not, it is very likely the shimming won't work well. The final B0 deviation should be below 1 Hz after shimming. If not, check whether the sample is inhomogeneous. Poor quality NMR tube, air bubbles, or insoluble substances can cause poor shimming. If the sample is fine, you may try to following options, then redo topshim.Fir
Excel file NMR_title_files.xlsm, updated 07/2020.
This excel file can help to document and organize all your NMR experiments by saving all the title files in an excel sheet.
Function: Search the "title" files from a selected folder, and collect title contents in a Excel worksheet.
1). Make sure the Microsoft Excel program on your computer is macro enabled. Instruction available in the excel file.
2). Download and open the Excel file.
3). Press the search button.
4). In the browsing window, navigate to the desired NMR data folder, and click on OK.
5). In the pop-up search window type in keyword "title". The Macro will then generate a title list with path and the content in the title files.
Safety Policy Environment and Safety in Biomolecular Nuclear Magnetic Resonance Facility, University of Maryland, College Park: Responsibilities, Risks and Liabilities:
Staff members, Teaching Assistants, and Users will expose themselves to strong magnetic fields (maximum of 14 Tesla) from the NMR superconducting magnets, while they are working around the spectrometers. To the best knowledge of the NMR community, no known health hazard has been reported when one is exposed to such field, in the past twenty years. However, there is no guarantee that future findings may show otherwise.
Any person with metal implants, such as heart-pacers, should not work or enter the NMR labs. The strong field and the radio frequencies of NMR spectrometers are known to interfere with heart-pacers.
Keep all loose metal objects at least ten-foot from the magnets. The strong magnetic field attracts any loose paramagnetic metal objects nearby. The collision force is so strong that it can induce a structural collapse of the magnet, which in turn causes spontaneous boil-off of the super-cold liquids in the magnet. A person around the collision (magnet) can be injured.
Use proper procedure and obey safety policy when dealing with liquid nitrogen and liquid helium. Then superconducting magnet contains liquid nitrogen and liquid helium. Contact with these cold liquids will cause severe burns to the body. Safety policy must be complied with during transportation and refilling of the magnet with these liquids. During the refilling of liquid helium, the operator must be very careful and always maintain proper balance when stepping up to the platform (no more than 3 feet in height). Falling from the platform could lead to body injuries.
The prospective users should read ‘responsibility, risks and liabilities’ and fully understand the potential danger, implication and risks described. The staff members in the NMR facilities, the Department of Chemistry and Biochemistry or the University of Maryland is not responsible or liable for any possible misshape caused by any user negligence. By reading this, the users will behave responsibly and follow all the proper procedures as described in this form and the published NMR facility policy of the department.