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This is a new feature of the website!

The previous FAQ is still posted as a PDF file here.  We are migrating that information into this FAQ.

As always, you can reach us at support@nmrbox.org with any questions or suggestions you have.

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When connecting to NMRbox via RealVNC for the first time, or after a reboot of the server, the screen resolution will likely be smaller than you desire. The NMRbox team has built a tool to allow for quick screen resolution changes which works without affecting any ongoing processes. The tool can be launched in a few different manners:

  1. By going to the Xfce menu bar (in the upper left hand corner of the screen by default) and selecting "nmrbox-util" and then "Resolution Changer"
  2. By going to the Xfce menu bar and selecting "Settings" "Display"
  3. By running "resolution_changer.py" from a Terminal window

Once launched simply select the desired resolution and press "Apply". The window will stay open for easy adjustment to a different resolution if desired. Press "Exit" whey you are finished.

It is sometimes desirable to have the screen resolution be slightly smaller your monitors resolution, in those cases select the "Scale resolution by 90%" radial button.

If you plan on spanning your RealVNC window over two monitors you should select the "Double Horizontal Width" radial button. Note that by default the RealVNC window will only be displayed on a single monitor. Please read the FAQ on how to have RealVNC span two monitors.

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Acknowledging and referencing NMRbox is important for continuing financial support from NIH. If you use NMRbox for any data processing or analysis for a published study, please cite our Biophysical Journal article and acknowledge the NMRbox Center as shown below: 

NMRbox: A Resource for Biomolecular NMR Computation. Maciejewski, M.W., Schuyler, A.D., Gryk, M.R., Moraru, I.I., Romero, P.R., Ulrich, E.L., Eghbalnia, H.R., Livny, M., Delaglio, F., and Hoch, J.C., Biophys J., 112 1529-1534. PMID: 28445744, DOI: 10.1016/j.bpj.2017.03.011

"This study made use of NMRbox: National Center for Biomolecular NMR Data Processing and Analysis, a Biomedical Technology Research Resource (BTRR), which is supported by NIH grant P41GM111135 (NIGMS)."

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No! Once the VNC Server session is started it will remain running until it is either explicitly closed or the NMRbox server is power cycled. You can connect and disconnect to the same VNC session multiple times and from multiple devices. Calculations that are being performed continue to execute even when the VNC Viewer is disconnected. This can be convenient when using NMRbox from different locations such as work and home.

Note that you can connect to your NMRbox VNC Session multiple times concurrently from the same or different devices. In this case the Desktop environment is shared (all connections will view the exact same screen, including mouse movements).

If your VNC session is not behaving properly you can explicitly kill it by opening a terminal and entering the command "kill-vnc-server" and then selecting the server to kill (generally there will only be one selection).

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If the graphical windows in a VNC session start behaving oddly, the easiest fix is to stop your current session and create a new one by reconnecting with the VNC viewer. Note that merely disconnecting your VNC viewer leaves the graphical session running so you can just pick up where you left off. To stop a VNC session, open a Terminal window and type: kill-vnc-server. You'll be presented with a list of sessions; if you're executing kill-vnc-server within a VNC session, the current session will be annotated. Just select the desired session to close and press Enter. If you run kill-vnc-server from a VNC session the VNC connection will be disconnected and you will need to reconnect via Real VNC Viewer.

Note that running kill-vnc-server is akin to logging out and back into a computer and thus any currently running jobs will be lost.

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You can use the password reset form at https://nmrbox.org/forgot-password to reset your password.

It is important that you do not attempt to login with the wrong password over and over again. Too many failures will cause your account to be blacklisted for a period of time. 

Alternatively, email us at support@nmrbox.org for assistance.

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You have several options:

  1. scp
    You can connect to your named NMRbox VM (username@username.nmrbox.org) via ssh and use scp.

  2. Globus
    See our Globus guide.

  3. DropBox
    Open a terminal and type: dropbox start -i
    This will launch the DropBox installer.
    Follow the instructions to install and login.

  4. RealVNC

            > To SEND files from local computer to NMRbox    

                    hover mouse near top center of VNC window
                    click on “File transfer” icon                    
                    follow directions

            > to FETCH files from NMRbox to local computer

                    click VNC icon in status bar (top right, next to username)
                    click menu icon in top right of pop-up window
                    select “File transfer…” menu item
                    follow directions

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You must use Real VNC Viewer - no other VNC Viewer will connect to NMRbox!

NMRbox utilizes a commercial VNC server from the company RealVNC. The commercial version of RealVNC provides several benefits as outlined here, but the only way to connect to NMRbox is with a VNC Viewer from RealVNC. The good news is that the NMRbox team has purchased licenses for RealVNC server and NMRbox Users only need to download the free VNC Viewer from RealVNC which runs on almost any device.

Note that you only need to install the RealVNC Viewer and not the server portion named RealVNC Connect.

  • Mac users: Download RealVNC Viewer from here and install.
  • Windows users download RealVNC Connect from here and install. During the installation de-select the VNC server checkbox.

Benefits of RealVNC server:

  • Free. RealVNC Viewer is free for all platforms and runs on almost all devices.
  • Full encryption. All connections with NMRbox are fully encrypted.
  • Single sign-on. Your NMRbox username and password are used to logon, unlike open-source VNC servers which require the User to create a separate, unsecure, login which resides in the users Home folder.
  • Daemon mode. There is no need to login via ssh and start a vncserver session manually. VNC server sessions are started automatically when you login via RealVNC Viewer.
  • Built-in file transfer. Files can be transferred into and out of your NMRbox account from within the RealVNC Viewer program.
  • Local printing. The default printer on your local computer is mapped to your NMRbox account allowing Users to print from within NMRbox to your local printer.
  • Full screen mode and multiple monitors. RealVNC supports Full Screen mode with and without scaling and allows the display to span multiple monitors.
  • Performance. The commercial RealVNC Viewer / Server combination has excellent performance.
  • Persistent sessions. Once started the VNC server session will remain alive allowing the User to connect and disconnect as often as they like from any location or device.

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We will make every effort to not shut-down services to NMRbox VM PaaS, but occasionally the systems will need to be powered off for maintenance. We will make every effort to notify users ahead of time with any scheduled outages. When possible our preferred time for maintenance will be on Monday’s at 7:30 AM Eastern Time (New York), but reserve the right to handle maintenance at other times as well.

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The use of a Terminal Emulator (often called “shell”, “terminal”, or “command line”) is critical to utilize many of the programs within NMRbox. We have created a document on how to use the terminal which can be found on the Documentation page of the NMRbox website. In addition, the sites below are good sources of information and Ryans’s Tutorials has some good tutorials.

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Newer laptops often have very high resolution screens - even 4k displays!. On Windows and OSX the size of menus, icons, and fonts are scaled to be larger so they are readable on such high resolution screens. However, when connecting NMRbox VM PaaS the menus, icons, and fonts may be so small they are unreadable. To fix this issue open a terminal and run “resolution-changer.py” and choose a reasonable resolution for your screen size, which may be considerably less than the actual screen resolution, such as 1920x1080 when using a Retina or 4K laptop. The NMRbox window will be small and hard to read at this point on your high resolution screen. Then go to the RealVNC Viewer Toolbar and select Full Screen or play with the scaling setting to stretch the screen size larger and hence make things easier to view. Note that you may need to select / deselect the “Scale to window size” and “preserve aspect ratio” from the Options window under the “Advanced” window and “Display” tab to optimize your window. With a bit of playing around you should be able to find settings that suit for laptop.

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Go to https://nmrbox.org and press “Sign up for an account” and fill out the form. You will receive a confirmation email. NMRbox accounts are manually verified and can take up to 2 business days to process. Once your account is validated you will receive an email with instructions on how to access your account and connect to NMRbox.

Note, if you have any questions or do not receive any of the emails referenced above, please contact us at support@nmrbox.org to ensure that your account request is properly handled.