Dear Bernhard, so I'm a bit late with this, since your problem is solved already. Nevertheless I documented at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Example:_installing_a_64bit_nightly_CentOS5_binary_build_on_64bit_SL6.1 the installation of the CentOS5 binary build on my SL6.1 64bit notebook for you. Admittedly, it is not as easy as running a Windows installer, but I doubt that with other flavours of Linux it would be easier - only different.
I noticed that you modified LD_LIBRARY_PATH at one point, and I found that this leads to all kinds of havoc downstream, until finally only elves can help you. HTH others, Kay
