Installation Guide For Bruker's Topspin 4

1 1On Apple Mac s only Intel Core Two Duo chips aresupported; the older (around2007) Intel Core Twochips are not supported. As long as your computerisn t more than8or so years old; it should Bruker used the Flexlm software tomanage licenses; this has switched to software from CodeMeter. 3In the past there was a bug with certain web-browsers (Chrome and Edge) regarding the licenseactivation through Topspin . If it doesn t work, thesuggested fix is to use Firefox or Safari. Paste the urlgiven into the new you have a departmental IP address you can accessthe server. If you configure access to the departmentalVPN, you can gain access from anywhere in the world;this is my prefered Guide For Bruker s NMR Service, Dept. Chemistry, Cambridge UniversityMarch26,2020 This document attempts to Guide the user through the intricacies andoptions of installing Topspin software. This is a work in progress;please let me know if you have any additions or corrections to , latest version of Topspin , version4has been released under a free for academic use license and so the department no longer issueslicenses; they are issued directly from are various packages that not only process your data, but cando some quite in-depth analysis; including structure verification andelucidation.

2 (With the addition of additional purchasable modules)It is now available for Microsoft Windows (version7and above),Linux (Centos5) and Apple OS X (Intel based)1platforms. In the pastyear it has become free for academic use; this version has(almost)allthe functionality of the commercial InstallationYou will need to register withBruker,2; fire up a web-browserand go to:- login and register ; then jump through all the hoops to createan registered go to :- click Free Academia License and then Request personal licenseticket now .3 You do not need to download the software from Guide for bruker s Topspin 2 Figure1: Topspin Super-User As long as you get get access to the NMR backup server, nmr-fs .Obtaining The SoftwareIn order that the bandwidth of the department is conserved (whichdoes cost a reasonable amount per gigabyte), I ve downloaded in-stallation packages onto our backup server. You can find them in thelocation :-\\ \software\TopspinTo access the server, follow the instructions on :- the relevant file to your computer.

3 There is also an iso file which provides a complete image of the Installation DVD, whichserves all platforms. You will need to read the manual of your DVDburning software to correctly write this to a disc. Just simply copyingthe file will not work. Or you can install software that will allow youto mount the ISO file to your computer; it will appear like a diskdrive and you can install the software from comes with a super-user account to administer Topspin , thiswill default to the account you are logged is one of Topspins little quirks; it has its own security systemto prevent tampering with the software; so it creates its own pass-words that are separate from the operating system. The passwordyou type heredoesn t have to be the same as your login password and prob-ably shouldn t be, as the password is stored in a file on the disk and could you begin; you should log in to your system with an accountthat has administrator privileges.

4 Double click on the .exe you down-loaded above and follow the instructions to install the software. Youwill have to click through some issues related to the security of yoursystem, before you can install the Guide for bruker s Topspin 3 Figure2: Install locationFigure3: Customise InstallFigure4: Configure firewallFigure5: OS X install screen5 This directory is hidden by default and you may notbe able to browse to it. So in the finder window click Go and Go To Folder and type in/optThe Installation will also pause to display a release letter and it maynot continue until you close it!You can chose to change the location of the Installation if you wish;but unless you have good reason; its probably best to stick with asked, unless you have good reason choose the Data Process-ing only option. (It is possible to change the install location, trim thesize of the Installation , or install a few extras by choosing customise,but unless you are certain of your needs, its best to go with process-ing only.)

5 Figure3 Mostly it is just a question of accepting the default Installation will ask you if you wish the windows firewall to you are familiar with how to administer the firewall and areprepared to spend some time doing it yourself; say yes here! If youmistakenly say no my advice is to abort the install and start again..Reboot your computer and test whether the software starts. Once itdoes, please now go to the sectionFirst UseMac OS XDouble click the to mount the Installation image;then double-click the file to start the continue until you get to the Installation type. Here you cancustomise the type of Installation if you wish; although there is actu-ally little reason to do so. You can only really choose to not install aC complier and CMC Assist. There s no option to change the installlocation either, the software is put in/ click through the main problems occur with the security settings on OS X Catalina .Bruker is not on the the approved list of developers, and so thedefault security settings will prevent the installer running.

6 To getaround this problem, type Security into the spotlight search, select Security and Privacy , go to the General tab and allow the softwareto Guide for bruker s Topspin 46I used Oracle VirtualBox in all your computer and check Topspin starts. Once it does, pleasenow go to the sectionFirst CentOS InstallationIt is important that you install Topspin onto the correct Linux distri-bution; the supported versions are CentOS7and5. Topspin is nowa64bit application, so you should install that version of linux. TheCodeMeter software requires a linux distribution that supports RPM packages. You can download it from the following you are determined to install it under your own non-supporteddistribution of Linux; I d suggest installing into a virtual machine,you may have to fix a lot of dependencies, which might affect yourstandard operation.. I ve tried installing Topspin on various clientOS virtual machines running under Open SUSE and OS to install, for the most part its just simply clicking through the de-fault options; you can change the install location, and the customisethe components you install; but I would recommend sticking with your computer and test whether the software starts.

7 Once itdoes, please now go to the sectionFirst Useinstallation Guide for bruker s Topspin 57 This will actually keep appearing each time youstart the software unless you click the Do not display : ExpinstallFigure7: cf stage1 Figure8: CF stage2 Figure9: CF routingFirst UseThe first time you start the software you ll need to register it. You canpaste in the license code you received above; or request a new of December2017there is still a bug when activating the it usingMicrosoft edge or Google Chrome. If it doesn t work, install Firefox,go through the process again and paste the URL from Edge or Firefoxinto it actually starts; there will be the usual license agreement youwill need to click Ok software will now present you will the dialog box shown prompts you do something called expinstall and cf . Its a goodidea to do this, as some our automated processing requires it to work. Expinstall sets up some standard parameter sets, automation pro-grams and plot layout files for use with Topspin ; cf can configure avirtual spectrometer use by the simulation programs within the soft-ware.

8 Its not strictly necessary to do a cf to use the software, but Igenerally do; just in cf Choose cf, then from the chooseAvance 600 MHz(which is of a datastation type) and click Edit at the bottom of the window. You willnow be shown a sequence of screens detailing information about thisconfiguration mostly its just a question of finding the default Next button to first screen has a short summary of the configuration; you canmake changes here; but it probably isn t necessary. Click next will then be shown a slightly intimidating routing diagram; justclick save and close. Next there s a summary of the hardware andsoftware configured, just click Next cf configuration is now finished; you can now run through the expinstall routine by clicking the button. You don t need to botherwith the other options; edscon and so Guide for bruker s Topspin 6 Figure10: Experiment InstallationFigure11: Expinstall TypeFigure12: Expinstall optionsFigure13: Expinstall FormatConfiguration expinstall Next you need to run through the expinstall routine; probably came to this point by clicking a button; if you have nobutton to click, you can typeexpinstallat Topspin s command its mostly just a matter of clicking Next to go through eachstep.

9 Note, you can run the command multiple times to install all thedifferent types of the default options of what to the paper format; I tend to choose A3as that s what we usein our service layouts. The software will prepare the installationdefault layouts Finish . It will take a bit of time to copy all the standard pa-rameter sets, au programs last window of the routine prompts you to schedule a backupof the Topspin Installation . This will be useful if you spend a lot oftime getting your layouts and parameter sets just the way you can safely ignore the option and click close . Backups can bemanually triggered by typingnmr_saveat Topspin s command Guide for bruker s Topspin 78I have a Centos one that takes up less than32GB ofspace; enough to fit on a USB stickAdvanced InstallationInstallation to a virtual machineI have installed Topspin to Windows and Linux virtual machinesrunning under Windows, Linux and OS X operating systems us-ing Oracle s Virtualbox software.

10 It works very nicely; as long asyour computer has enough RAM installed. As the virtual machine isportable;8it makes it possible to transfer your working environmentbetween computers if you service plot layouts and au programsWe have a number of layouts and au programs to automate yourwork flow; to install them follow the instructions will periodically be updated; so please occasionally check there is no guarantee that they will work flawlessly with yourdata; always work with a copy of important data as we accept toliability of loss from using these programs. Any bugs or requests forfeatures; please contact plot layoutsCopy all the layouts beginning with service from :-\\ \software\service-plotTo :-$TOPSPINHOME$/plot/layouts/Where$TOPSP INHOME$is :-c:\Bruker\ a Windows PC and/ OS X or au programsCopy all the files beginning with serv from :-\\ \software\service-auTo :- Installation Guide for bruker s Topspin 89It calls different sub-au programs to process eachdifferent type of experiment$TOPSPINHOME$/exp/stan/nmr/au/ src/user/Using the au programsTyping the name of the au program will run theservice-master-proc9first.