Essentially, OpenChrom now seems a lot easier and more natural to use.
The installation is the same as before (I've copied the old post below):
1. Install Java v1.7 (need > 1.6)
You can either use openjdk 7 or (Oracle) Java. See here for a general guide to installing Oracle/Sun Java.
As for openjdk, you can easily install it:
sudo apt-get install openjdk-7-jdk
(the openjdk-7-jre package is enough if you don't want the full developer's kit)
Make sure that you've selected the right version:
sudo update-alternatives --config java There are 7 choices for the alternative java (providing /usr/bin/java). Selection Path Priority Status ------------------------------------------------------------ 0 /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java 1061 auto mode 1 /usr/bin/gij-4.4 1044 manual mode 2 /usr/bin/gij-4.6 1046 manual mode 3 /usr/bin/gij-4.7 1047 manual mode 4 /usr/lib/jvm/j2re1.6-oracle/bin/java 314 manual mode 5 /usr/lib/jvm/j2sdk1.6-oracle/jre/bin/java 315 manual mode 6 /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java 1061 manual mode *7 /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java 1051 manual mode
2. Get openchrom
sudo mkdir /opt/openchrom
sudo chown $USER /opt/openchrom
cp * -R /opt/openchrom
chmod +x /opt/openchrom/openchrom
alias openchrom='/opt/openchrom/openchrom'in your ~/.bashrc and source it.
A few notes:
You can now start OpenChrom by running
openchromfrom the command line.
You can install plug-ins, e.g. to open Agilent files, by going to Plugins/OpenChrom Marketplace. Plugins will typically run for 30 days, but can be unlocked for perpetuity by adding a serial key, which is free. Add license keys by first registering on the openchrom website, going to http://www.openchrom.net/main/content/plugins.php, and clicking on the plugin you want a serial key for. You can then enter that key by going e.g. Window/Preferences/Converter in the OpenChrom software.
Everyone has their own idea of what a good piece of mass spec software should look like, and I suspect that OpenChrom caters to them all. Layouts are called Perspectives here. On the flip side, if you accidentally use a perspective that doesn't suit you, you may be incredibly frustrated until you figure out what's going on.
I like wsearch32, so my preferred view is to go to Window/Perspective Switcher -> Chromatogram MS (exact).
Opening spectra is much easier than before: now simply go to File/Open Chromatogram (MSD) and click on the file (or directory structure in the case of e.g. Agilent .D directories) and open:
Anyway, openchrom is getting better, is easier to use, and is still the only open source program that I know which can handle such an array of proprietary formats. Also, it can export data in both .csv and .xls formats, but you will need to install plugins for that, which is luckily very simple.