Transfer data to NMRbox via Cyberduck

Protocol: Transferring Data from a Linux Machine to NMRbox via a Mac Running Cyberduck

Overview:
NMRbox has many useful features for processing and analyzing multidimensional NMR data, especially biological NMR data. As of October 2025, NMRbox requires the use of ssh keys. This protocol outlines the steps to generate and use ssh keys to transfer data from a Linux machine to NMRbox, using a Mac computer with Cyberduck as the SFTP client. We will set up SSH access to NMRbox both from the spectrometer and from the mac so that each option is available individually. We will then use Cyberduck on the mac to connect to both NMRbox and the spectrometer simultaneously. Finally, we use Cyberduck to transfer processed data from NMRbox to our mac. A similar approach is expected to work on Windows using WinSCP or Cyberduck, but we have not tested that.

  1. Prepare to set Up SSH Key Access for NMRbox
    • Log in to NMRbox at https://nmrbox.nmrhub.org/
    • Navigate to https://nmrbox.nmrhub.org/user-dashboard/ssh-key
    • You can also access this page by clicking on [My Tools] in the bar at the top and then clicking on [Manage SSH Access] in the left side bar.
    • Click on “Instructions on adding an existing key or generating a new one:” to expand the instructions in the middle of the page, above the box for entering keys.
  2. Check for an Existing SSH key on your mac
    • On your mac, open a terminal and run:
    • cat $HOME/.ssh/id_ed25519.pub
    • On Windows, this would be:
    • type "%HOMEDRIVE%%HOMEPATH%\.ssh\id_ed25519.pub"
    • If you see a long string starting with ssh-ed25519, you already have a key. If you get a “No such file or directory” message, proceed to generate a new key.
  1. Generate a new SSH key (if needed)
    • In your terminal, run:
    • ssh-keygen -t ed25519
    • Press [Enter] to accept the default file location.
    • If prompted for a passphrase, you may press Enter to leave it empty (recommended for personal computers). If on a shared computer, choose a passphrase.
    • If you see a warning that the file already exists, type [n] and press [Enter] to avoid overwriting your existing key.
  1. Add your public key to NMRbox
    • Display your public key by running the following in your terminal:
    • cat $HOME/.ssh/id_ed25519.pub
    • On Windows this would be:
    • type "%HOMEDRIVE%%HOMEPATH%\.ssh\id_ed25519.pub"
    • Copy the entire output
    • Go back to the SSH Key page on NMRbox, paste the key into the text box, and click [Save] below it.
    • You can add multiple keys (one per computer you plan to use) by pasting each on its own line.
  1. Generate your own SSH key on the shared spectrometer computer
    • Use the terminal on your mac to ssh into your own personal account on the spectrometer:
    • ssh username@magnet-name.chem.indiana.edu
    • Once logged in, follow the instructions above in sections 2-4:
    • ssh-keygen -t ed25519
    • Press [Enter] to accept the default file location, and [Enter] again to leave the passphrase blank.
    • Add your public key to NMRbox.
  1. Install and configure Cyberduck on your mac to connect to NMRbox
    • You can buy cyberduck from the mac app store or windows store, or you can download it for free from their website: https://cyberduck.io/download/
    • Open Cyberduck and choose “Open Connection” from the File menu or click the [Open Connection] button in the top bar of the browser.
    • In the connection dialog:
        • Select SFTP (SSH File Transfer Protocol) as the protocol.
        • Enter the NMRbox server address (e.g. zinc.nmrbox.org).
        • Set the port to 22 (default for ssh)
        • Enter your NMRbox username
        • Leave the password blank
        • Choose your SSH Private Key from the menu
        • ~/.ssh/id_ed25519
        • Click [More Options]
        • Set your path to your home directory or the data directory you have created inside your home directory, eg. /home/nmrbox/username/nmrdata/
        • Click [Connect]
    • Choose [New Bookmark] from the [Bookmark] menu to save this information.
  1. Configure Cyberduck on your mac to connect to the spectrometer
    • Choose “Open Connection” from the File menu or click the [Open Connection] button in the top bar of the browser.
    • In the connection dialog:
      • Select SFTP (SSH File Transfer Protocol) as the protocol.
      • Enter the spectrometer server address (e.g. magnet-name.chem.indiana.edu).
      • Set the port to 22 (default for ssh)
      • Enter your IU username
      • Enter your IU password or leave it blank to enter it when you connect
      • Set SSH private key to [None]
      • Click [More Options]
      • Set your path to the data directory in the shared spectrometer account. Note that the path is case-sensitive.
    • Choose [New Bookmark] from the [Bookmark] menu to save this information.
  1. Transfer data to NMRbox using Cyberduck
    • To open a new connection, choose [New Browser] from the file menu, and select the bookmark you made in step 6.
    • Once connected to NMRbox in Cyberduck, navigate to the directory you want to transfer data into.
    • To open a second new connection, choose [New Browser] again from the file menu, and select the bookmark you created in step 7 to connect to the correct spectrometer.
    • Inside this new window, navigate to the directory with the data you want to transfer.
    • Drag and drop the directory you want to transfer from the spectrometer window to the nmrbox window.
    • Be patient while the data transfers. It can take a long time.
  2. Confirm and organize files on NMRbox
    • After transfer, use cyberduck or an ssh terminal to verify that your files are correctly uploaded and organized in the appropriate directory on NMRbox.
  3. Transfer processed data files from NMRbox to your mac for publication
    • In the Finder, navigate to the folder you want to transfer data into.
    • Switch into Cyberduck and open a connection to NMRbox.
    • In Cyberduck, locate the data you want to transfer.
    • Drag the data you want to transfer from the Cyberduck window to the Finder window to copy it from NMRbox to your mac.
  4. Transfer raw data directly from the spectrometer to your mac, without NMRbox
    • Skip to step 7 to set up Cyberduck to connect to the spectrometer.
    • In the Finder, navigate to the folder you want to transfer data into.
    • Switch into Cyberduck and open a connection to the spectrometer.
    • In Cyberduck, locate the data you want to transfer.
    • Drag the data you want to transfer from the Cyberduck window to the Finder window to copy it from the spectrometer to your mac.
  5. Troubleshooting
    • If you experience connection issues, review the NMRhub SSH troubleshooting tips: https://nmrhub.github.io/NMRhub_SSH_Troubleshooting/
    • Ensure your public SSH key is correctly uploaded and that you are using the correct username and server address.
    • Make sure you have network access (VPN may be required if off-campus)
  6. Notes
    • You must generate and register a separate SSH key for each computer you use to access NMRbox.
    • The private key should remain only on your Mac; never upload it to NMRbox or share it.
    • If you only want to transfer data from the spectrometer directly to your PC you can skip all the NMRbox-specific instructions and skip to step 7
    • If you are comfortable using the command line, you may also use the terminal to transfer data directly from your own account on the spectrometer to NMRbox. On the spectrometer, I can open a new terminal window, and enter the following commands:
    • su myIUusername
cd /home/shared_account/Data/MyDirectory
scp -r myDataset username@zinc.nmrbox.org:~/nmrdata/

updated 6/20/25 KE

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