Frequently Asked Questions

Frequently Asked Questions

How Do I Get Trained to Use the Instruments?
  • To schedule a training, please contact our NMR Facility Staff
    • For VNMRS 600, Inova 400, Mercury 300 and Mercury Plus 300 instruments in Chemistry, please contact Bennett, Jeff or Woody. 
    • For liquids spectroscopy instruments Avance III 800, Avance III 600, and Avance 500 at MedSci, please contact Bennett - jbaddison@ucdavis.edu
    • For imaging instruments Avance 400 and Biospec 7T at MedSci, please contact Jeff - jhwalton@ucdavis.edu
    • For Avance 500 solid-state NMR in Kemper Hall, please contact Ping - pyu@ucdavis.edu
  • To gain access to both Chemistry and Medsci facilities, you must take the Magnetic Field Safety Training. To schedule a training, which will take approximately 15 minutes, contact Jeff Walton - jhwalton@ucdavis.edu
How Do I Schedule Instrument Time?
  • Visit the online scheduler. The NMR Facility Staff will grant you access to the spectrometers for which you have been trained.
  • Enter your username or email and password
    • If you do not have a scheduler account, you may create a new one. Please include Organization (eg. Chemistry, Molecular Biochemistry, Pharmacology, etc), position (eg. Professor, Postdoc, Graduate Student, Undergraduate, etc), and Principle Investigator.  
    • Your Magnetic Field Training Date field must also be provided. The format should be MMDDYYYY with no spaces or dashes.  The date you provide must match with our records.
  • Navigate to the Schedule / Bookings page.  You will have access to multiple calanders.  
    • For the Bruker Avance 400, Avance 500, Avance III 600, Avance III 800, and Biospec 7T, select the MedSci 1D Calander from the drop-down list
    • For the VNMRS 600, Inova 400, Mercury 300 and Mercury Plus 300 in Chemistry, select Chemistry Day (8am-5pm) or Chemistry Night calander (5pm-8am)
    • For Solid-State NMR Reservations on the Avance 500 instrument in Kemper Hall, select the Kemper 51 schedule.
  • Select the time block you would like to book. 
    • Minimum booking times are 15 minutes at Chemistry and 1 hour at MedSci.
  • Select a beginning and ending time for your usage
  • Provide an account number
  • Select "Create"
Can the NMR Facility Staff Collect My Data For Me?
  • Yes.  We encourage users to become trained so that they can collect data as needed.  However, upon request the NMR Facility Staff will collect your data for you. Please contact Bennett Addison for liquids spectroscopy, Jeff Walton for EPR or MRI, and Ping Yu for solid-state NMR.  Contact information is listed to the right.
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
How Should I Save And Archive My Data?

Chemistry Facility:

Users should copy their data onto the KONA NMR server, where they can later retrieve the files using sftp protocol from a personal computer.

Transfer data to KONA:

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/

Supplemental content

NMR Facility Information

NMR Facility Staff

Prof. Gary Smith - Director, NMR Facility

530-752-6168

gmsmith@ucdavis.edu

Dr. Jeff WaltonMRI / Imaging and Misc. NMR

530-752-7794

jhwalton@ucdavis.edu

Dr. Ping Yu - Liquids and Solids NMR

530-752-4396

pyu@ucdavis.edu