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Using Analysis with NMRbox

Using CcpNmr Analysis with NMRbox

If you don't want to or are unable to install CcpNmr Analysis on your computer directly, you can use it via NMRbox instead. NMRbox is a US-based scheme which allows you to run lots of different NMR software packages remotely via a virtual machine. Anyone with an academic or non-governmental institutional e-mail account can sign up: simply go to https://nmrbox.org and click on Sign Up to register. Note that it may take a couple of days for your account to be validated, as this is done manually. You will then receive an e-mail with your username and password.

RealVNC Viewer Installation

In order to access and view your NMRbox virtual machine, you will need the RealVNC Viewer which you can download here. It is available for many operating systems and should be fairly straight forward to install. Once you have installed the RealVNCViewer, open it and enter the hostname of one of our available servers listed on the user dashboard (e.g. carbon.nmrbox.org or neon.nmrbox.org, etc. - see below for more information on choosing your host). Confirm that you want to connect and enter you username and password.

Choosing a host to log into

NMRbox has many hosts and they are updated on a rotating basis which includes updates to software packages. Since CcpNmr Analysis is still being heavily developed we issue updates on a regular basis, so you will do well to use one of NMRbox's newest hosts. This will ensure that you are using a version of CcpNmr Analysis which has all the latest updates installed. Log into the NMR box webpage and go to the Hardware section to see the user dashboard. Here you will see a list of all the currently operational hosts. Choose one of the ones near the top of the list with the longest number of days till reboot to ensure you are using the latest version of CcpNmr Analysis. Obviously it is also good to choose a VM with low Utilisation.

Moving data into your virtual machine

There are several ways to do this. You can use scp (secure copy) on the command line, an ftp program such as Filezilla or CyberDuck. Alternatively, you can use the VNC Viewer directly: move the mouse to the top of the window to see a little drop-down menu and click on the Double Arrow Transfer files icon.

Opening CcpNmr Analysis

Open a terminal using the Terminal icon at the bottom of the screen. Then type assign to open CcpNmr AnalysisAssign. You can open AnalysisSctructure with structure, AnalysisScreen with analyisisscreen and AnalysisMetabolomics with metabolomics (note that screen will open a different program!).

Remember that the NMRbox virtual machine is a Linux machine, so even if you are accessing it from a Mac, you will have to use the Ctrl rather than the Cmd button for shortcuts or to modify the mouse behaviour.

Changing the screen resolution and using two monitors

By default the screen resolution when you connect to NMRbox is rather low. You can easily change this to match the resolution of your screen by following the instruction on the NMRbox FAQ on changing the screen resolution : go to the Xfce menu and select Settings and then Display, select your desired resolution and click on Apply. This will make life much easier when looking at your spectra!

It is also possible to set the display up to span two monitors (but it will treat these as a single display rather than as separate dual displays which is more common on Windows and OSX). Follow the instructions on the NMRbox FAQ page. It involves a number of steps and varies slightly depending on your operating system.

Trouble-shooting and logging out

If your colours and rendering look strange, then this is usually a sign that there is a problem with the VNCViewer connection. NMRbox recommends logging out (click on your username in the top-right hand corner and then on Log Out... and Log Out. This will end your session. You can now reconnect from VNRViewer.

An alternative way to end your NMRbox session is to move the mouse to the top of the VNC Viewer window to bring up the drop-down menu. Click on the End session blue cross. This will break your VNC connection, but without logging you out of the NMRbox virtual machine. This way you can leave something to run on your NMRbox virtual machine without being connected. However, if you are having trouble with the rendering, this will not be sufficient and you will need to log out fully in order to restore correct rendering.

The NMRbox FAQ page is also very helpful if you run into problems.

Using NMRbox as part of a CCPN Workshop

If you are using NMRbox as part of a CCPN workshop, then please make sure you register for the workshop on the NMRbox events page. This will ensure that you automatically have access to all the tutorial data which you will need for the workshop.