Frequently Asked Questions

Frequently Asked Questions

How Do I Get Trained to Use the Instruments?

How Do I Schedule Instrument Time?

What are the Spectrometer Recharge Rates?

What are the NMR Facility Safety Policies?

What grants should I cite for data collected in the NMR Facility?

Can the NMR Facility Staff Collect My Data For Me?

How Should I Save And Archive My Data?

Why is my Shim Bad?

NMR Tube Selection, Care, and Re-use.

 

How Do I Get Trained to Use the Instruments?

To gain access to both Chemistry and Medsci facilities, you must:

Create a PPMS account. Go to https://ppms.us/ucdavis/, click on NMRF, and create an account. 

Submit a safety training request. Download the form, print, read, and sign it. One of the Facility staff will contact you to schedule safety training lecture. Bring the signed form (Signed by both you and the safety training lecturer) with you to the training.

After Safety Training, request training on the instrument. No Instrument training will be done without safety training. Permission to schedule will not be given until training is complete.

Download Detailed Instructions: Registration Instructions.pdf

How Do I Schedule Instrument Time?

Once you have an account in PPMS (See Above), and the NMR Facility staff has given you permission to schedule, scheduling is done through PPMS

After entering your kerberos ID and password, click on the book tab. Select the instrument you would like to schedule. Click and drag across the times you would like to schedule.

Note some instruments may not be available to you depending on your training. If you cannot schedule an instrument, contact the facility staff as you may need additional training for that instrument.

What are the Spectrometer Recharge Rates?

See our current NMR recharge rates here

What are the NMR Facility Safety Policies?

Please review our safety policies here

What grants should I cite for data collected in the NMR Facility?
Instrumentation Grants

 

Can the NMR Facility Staff Collect My Data For Me?

Yes.  However we encourage users to become trained so that they can collect data as needed.  Also, as an educational institution, we view data collection as a valuable part of a student's education. But if needed, upon request the NMR Facility Staff will collect your data for you. Please contact one of the NMR TA's for Chemistry instruments, Ping Yu for liquids or solids spectroscopy in Med Sci,  and Jeff Walton for EPR in Chemistry or MRI in Med Sci.

How Should I Save And Archive My Data?

You are strongly encouraged to archive all your data using Google Drive as soon as your data acquisition is complete. Do NOT use a USB flash drives because of the potential to infect the system with malware and/or viruses.

Chemistry 400:

The NMR data on the CHEM400 are automatically uploaded to the shared google drive folder  PI400/username. On other instruments you’ll need to manually upload your NMR data to the google drive.

Chem 600, :

Users can upload their data to the KONA server from the Red Hat Linux Work Stations (VNMRS 600, Inova 400, Mercury 300, Mercury Plus 300).  

1.  On the NMR Workstation, double click the KONA folder on the Desktop

2.  When prompted, type in the password provided at the instrument (not provided online for security purposes, but the password is posted at each spectrometer)

3.  In another window, navigate to your files you wish to copy.  Copy your files and paste them into your folder on the KONA server.  

MedSci 1D and Kemper Hall

Transfer of data to the NMR server:
Data transfer from Facility Windows 7-based spectrometers (Bruker 600, 800)

Using a Windows 7 PC host computer, you can move data directly to the NMR server just by using the mouse to drag and drop in Windows Explorer. The server is drive S, A.K.A. share$. If you don't already have a folder on this drive, use File > New > Folder in Windows Explorer to create your own data folder on the server. Please use your first initial and last name to name your folder, for example jwalton. Place the data on the server drive under Shared > Data > your_folder via drag and drop. Your files are now on the server. You will access this drive from your office via SFTP (see below).

Data transfer from Facility Linux-based spectrometers (400, 500, 7T, 500 Solids)

1) Open a Konqueror window by double clicking on the home folder icon.

2) Repeat so that you have two windows open

3) In window 1, go to your data folder /opt/pv4/data/$USERNAME/nmr (or for topspin, /opt/topspin/data/USERNAME/nmr)

3) In window 2, in the address line type: sftp://kona.ucdavis.edu. Hit Return.

    - Note, it may be useful to you to create a shortcut for the FTP server onto your desktop.  Simply click and drag the link to the Desktop and select Copy Link Here

4) Enter user name and password.

5) Navigate to your folder on the server.

6) Drag and drop files/folders you want to move from one window to the other.

You may need to enter the user name and password more than once.

Retrieving your data from KONA:

For Windows:

1.  Download SSH/SFTP Secure Shell Client. Here’s one of many links:

https://shareware.unc.edu/

Find SSH/SFTP Secure Shell – 3.2.9 and click download

2.  Once installed, open up SSH Secure File Transfer Client

3.  Click on Quick Connect and enter the following:

Host name: kona.ucdavis.edu

Username:  nmrftp

Port: 22

4.  When prompted for the password, use the same password you used to copy files to KONA:

The left side of the interface is your local computer while the right side is the ftp server. Use the Secure Shell interface to copy data from the server to your computer. When done, terminate the connection to the server.

For Mac Users:

1.  Download and install Cyberduck.

https://cyberduck.io/?l=en 

2.  Open up Cyberduck and enter the following information:

Connect to: kona.ucdavis.edu

Username:  nmrftp

Port: 22

Directory: just leave it blank

3.  When prompted for the password, use the same password you used to copy files to KONA:

4.  Click on Connect and you should now be able to see all the NMR folders. The left side of the interface is your local computer while the right side is the ftp server.

 

Additional notes:

1) The server is for temporary data storage only. Data you place there should be copied to your office computer. Files will be deleted from the server by the system administrator on a regular basis.

2) You must use secure FTP A.K.A. SFTP (not plain FTP) to connect to the NMR server. You must therefore use an FTP program that supports secure FTP.

3) You must be connected to the campus network either through ethernet or through a wireless router that has a static campus IP address.  Currently, access to kona.ucdavis.edu is blocked for mooblenetx and eduroam campus wireless networks, and for any off campus internet connection.

 

Can I Reuse NMR Tubes?

The quality of NMR Tubes can make a big difference for you data, however good tubes can be expensive.  It is possible to reuse your expensive NMR tubes with proper cleaning.  To learn how to properly clean your NMR tubes, check out this page from Wilmad Lab-Glass:  https://www.wilmad-labglass.com/Support/NMR-and-EPR-Technical-Reports/Proper-Cleaning-Procedures-for-NMR-Sample-Tubes/