NMR software

There is a wide variety of software available for processing your NMR data, with some being free and others not.

 

Bruker TopSpin 3

TopSpin can be installed as a virtualised application on any University-managed Windows machine, or locally on your own PC on either Windows. MacOS or Linux.

AppJ/Jukebox/Cloudpaging Player/Apps Anywhere

TopSpin 3 can be installed on any University-managed Windows machine using AppJ. You do not need admin rights to do this, and it will work for >95% of your routine processing needs.

At the moment compilation of AU programs does not work, so there will be some "setdiffparm" error messages during DOSY processing, but it will still work. Operations such as completely automated processing will not be possible (proc_* programs), but typically you would do this manually anyway (phase, baseline correct etc.). It also means that some advanced processing will not be possible at all, e.g. covariance, DECRA and processingo of interleaved IPAP datasets.

How to install TopSpin locally (all platforms)

TopSpin 3 is currently free for academic use (registration required), and this software can be installed on to both University-managed and personal machines. Before doing anything else, you need to have "proper" admin rights requested via ISS. While local admin rights are enough for the initial installation, they are not enough for the initial configuration step.

The files for installing it are stored in: \\silo\FST\CH\NMR\Software\TopSpin, but if you have any problems contact Dr. Geoffrey Akien.

The below instructions refer to TopSpin versions 3.5 patch level 7 (3.5pl7). If a new version of TopSpin has been released since then, the numbers may be slightly different but the instructions will still be the same.

  1. Ensure you have admin rights.
  2. Obtain the correct installation files for your needs - currently the "TS3.5pl7 (free)" folder.
  3. Open the correct installer for your OS: Windows - "install.cmd"; MacOS - "TopSpin-3.5pl7.dmg"; Linux - "install".
  4. Click "Yes" to all the dialogs, and close the "rellet.pdf" file when it is opened to allow the installation to continue. Accept the default location and select "customise". We want: TopSpin, CMC-a (optional), NMR-Sim, NMR-Data (optional), FlexLM, NMR-Guide (useful), Dynamics Center (optional but highly recommended if you ever intend to do DOSY experiments).
  5. Accept the default NMR Super User (should be the username you are currently logged in with). You can leave the password field empty for convenience on your own computer.
  6. Accept the default locations for the example data and FlexLM, and say yes to configure the firewall automatically - FlexLM won't work properly otherwise! It takes approximately 10-15 minutes to install completely.
  7. Copy the license.dat file into the right place: Windows - "C:\flexlm\Bruker\licenses"; Linux: "\opt\flexlm\Bruker\licenses". For MacOS use Finder and open "TopSpin Utilities", "Applications", and run "Install License", telling it the location of the license file.
  8. The first time you open TopSpin it will prompt you to run "expinstall". Accept the defaults - it will take 1-5 minutes to set this up. If you only have local admin rights you'll get "Access error 5" - go and request them from ISS before trying this step again.

MacOS issues

Note that 3.5pl6 has issues with Sierra (MacOS 10.12), but these can be fixed with the files provided by Bruker (registration required): https://www.bruker.com/cgi-bin/bkb/show_bug.cgi?id=13882. This does not appear to have been resolved in 3.5pl7.

Alternatively, the same files are located in the "TS3.5pl6 - MacOS patches" sub-folder.

Linux installations

Note that officially TopSpin 3 installations are only supported on CentOS, but it is possible to install it on Ubuntu with some work.

A summary of these instructions will be included here in the future, but be aware that these are likely to not necessarily work with your particular version of your particular flavour of Linux. In particular, TopSpin uses 32-bit libraries for some applications, and the handling of these libraries in different 64-bit distributions can be rather varied - YMMV!

Licenses

We have licenses for 20 simultaneous users of TopSpin and CMC-assist, and two licenses for fully-featured NUS processing. Those two NUS licenses are checked in and out as you process your data, so if you can't process your NUS data immediately, try again in a minute or so's time.

The 21st person to launch TopSpin will revert to the free for academic use licensing. They will be unable to use CMC-assist, to process 3D and higher NUS data, and NUS reconstructions will use a different algorithm (IST). This is unlikely to affect most users.

How to handle your data

Note that to you manipulate your data in TopSpin, you MUST copy your NMR data from the silo into somewhere where you have write permissions - usually on your own computer. For convenience, you can then add this folder to the file browser pane on the left.

If you have a lot of 2D data, you will find that your personal filestore (aka "H drive") will fill up pretty quickly, so you can either request more space from ISS (the best way as ISS backs it up for you), or store it locally - this will not be backed up automatically! If you have admin rights on your Windows PC this can be anywhere at all, but if you don't, C:\Users\Public Documents\ does not need permanent admin rights. Only do this if you have a robust backup strategy in place!

 

ACD/NMR Processor Academic Edition

ACD/NMR Processor Academic Edition is a freeware package for processing your NMR data, and can be installed directly on any Windows machine using AppJ. You can also install it the conventional way on personal machines using the installer on the filestore at \\silo\FST\CH\NMR\Software\ACD_Freeware, but you will need admin rights (a local admin account is enough).

Compared to TopSpin 3 it is less powerful, but it can be easier to use (at least initially) because the learning curve is shallower.

In contrast with TopSpin, you can also open your NMR data directly from the network server without the need to make local copies of your data. You will still need to save your processed data locally though.

 

SpinWorks

Another free alternative for (mostly) Windows is SpinWorks. Although the appearance is somewhat dated, it contains some very powerful spin simulation tools.  You will also need admin rights to install this on University machines.

 

Mestrelab Mnova NMR

Mnova is a popular NMR processing package, but this is not free. A small number of individuals in the department use it, but these are currently paid for separately. Should this number increase it may become feasible to organise this centrally.