I have a persistent Kubuntu 8.10 on a 16Gb flash drive, on which I have been running the likes of Coot, iMosflm and CCP4. I have used my setup to process two datasets via MolRep.
There are plenty of resources on the internet telling you how to set it up. e.g http://www.pendrivelinux.com/ http://www.linux-usb.org/ https://wiki.kubuntu.org/LiveUsbPendrivePersistent It was relatively quick to set up, but it took a week to work out some problems. The main one being that with limited space on the thumb drive, one cannot do a complete update of Kubuntu. Therefore many libraries are missing and dependancy errors crop up during crystallography software installation. It's not too difficult a problem to deal with if you are familiar with installing apps on linux. And by partitioning your drive with FAT32, and two ext3 partitions (one for the root, and one labelled "casper-rw") before creating the linux boot-stick, you can have a bootable linux usb stick with the ability to share files with a windows machine (fat32 partition) and enough space to install those behemoth crystallography apps. And I managed to do all this with minimal linux experience. (The only issue I haven't yet resolved is with graphics drivers. Its a trivial task to install the appropriate drivers, but it seems every time I boot up Kubuntu, I have to run 'x-config' and restart the x-server to get the Nvidia drivers to work, which is necessary for Coot, at least. An inconvenience every time I start linux, but not impossible). Im not familiar with setting up or running virtual machines / emulators, but they might be a simpler, more versatile option? But at least you can run graphical applications with ease (pymol and coot run well once the nvidia drivers are working).
