iolite is run within Igor Pro as a series of scripts. Although ‘scripts’ sounds rather simple, currently these scripts are about 40,000 lines of code that handle everything from importing the raw data from your mass spectrometer, through to display and advanced data handling. These scripts are what are contained within your iolite v3 folder, along with a few other files, like standard files etc.

Igor Pro automatically reads these scripts when it starts up and then the functionality within the scripts is available to you the iolite user. If Igor Pro doesn’t read these scripts, you have just a basic installation of Igor Pro (which is very powerful by itself, but not what you need if you’re trying to work with mass spec data).

So, how does Igor Pro read these scripts automatically? Well, when Igor Pro starts it looks in two places for additional scripts to load. These are:

  1. In the Igor Procedures folder within the Igor Pro 6.x Folder within your Applications folder, or Program Files folder, depending on whether you’re on Mac or PC, respectively.
  2. In the Documents*\Wavemetrics\Igor Pro User files\Igor Procedures folder (*My Documents for PC).

By default, it should be the second of these two places, but for various reasons (related to installation and access privileges) it may be in the former folder.

There should be three iolite related files in one of these folders:

  • a shortcut (alias) file called IoliteAddOns that points to the Add Ons folder within your iolite 3 folder
  • another shortcut (alias) file called IoliteApplication that points to the Global Procedures folder within your iolite 3 folder
  • another shortcut (alias) file called IoliteMenuToggle.ipf that points to a file called IoliteMenuToggle.ipf within your iolite 3 folder

If you are having troubles with your iolite installation, it is likely due to some issue with these three files. Here are some possibilities:

  1. They might not be there;
  2. They may be pointing to the wrong version of iolite; or
  3. They might be in both of the folders Igor Pro checks at start up.

Let’s look at these three cases in order:

  1. The three iolite files are not in either of the folders. This assumes that you were able to find both folders, and they were empty, or contained other files, but no iolite files. This can happen for a couple of reasons. Firstly, the importer may not have had enough access privileges to put the shortcut files there (although usually the importer will tell you this). If this is the case, run the importer again, ensuring that you have full admin access. If after running the importer again you still have no iolite related files in either of these two locations, you can manually make these shortcut files. On Mac, right click on the Global Procedures folder within your iolite v3 folder and select Make Alias. Then rename the newly created alias as IoliteApplication. Repeat for the Add ons folder, calling the alias IoliteAddOns. Don’t worry about the IoliteMenuToggle.ipf alias at this stage. For PC, perform the normal steps required to make a shortcut file to the folders described. Then put these new alias/shortcut files into the Documents*\Wavemetrics\Igor Pro User files\Igor Procedures folder (*My Documents for PC). Then restart Igor Pro and see if iolite loads. If you weren’t able to copy the shortcut files to that folder, there is a permissions issue, and you should contact your local IT support to allow you to fix this.
  2. If the shortcuts are pointing to the wrong version of iolite (you can check by double-clicking on them to see where you end up), you can delete these files and manually create new shortcut files as described above. Or, you can change their target (here’s how on PC, and on Mac).
  3. If there are shortcuts in both locations Igor Pro checks at startup, you will get a “Function Compilation Error” telling you that some “name already exists as a function”. This case is the easiest to fix. Just look in both locations, work out which one has the shortcuts to the older version of iolite, and delete those shortcuts… BUT, if you’re unsure about deleting these files for good, just move them to your Desktop, restart Igor Pro and see if it works. If you got it wrong, you can always put the files on your Desktop back in the place you found them and delete the others.

If you are still unable to solve your installation issue after following the above guide, please check the iolite 3 forums which may have the solution. If not, please feel free to post to the forum. If you do not have a forum log-in, just download the free trial version of iolite. It will create a user account for you when you do, and you can use this login info to log into the forums.