According to a posting earlier this year (http://www.globalphasing.com/pipermail/sharp-discuss/2007-July/001848.html), to make coot run, you need to define CootSetup. Is there any reason it can't be enough simply to define the coot executable in helpers.local? (i.e. what else do people define in coot_setup.sh, apart from the path?) Cheers phx