If you tried to install Molekel under a recent version of Ubuntu or Debian you might have faced some difficulties. Here I report the step by step procedure to get it running. The biggest problem is that Molekel needs the old version of libstdc++6 which isn't in Debian/Ubuntu. All the commands that start with "sudo" are exectuted as root, so you have to get the root passwd before installing Molekel (or get your sysadmin to do it for you).
$tar -xvzf molekel4.3.linux.tar.gz (or $tar -xvzf molekel4.3.linux-mesa.tar.gz )
$sudo mkdir /usr/local/lib/molekel/
$sudo cp lib/* /usr/local/lib/molekel/
$gunzip libstdc++-libc6.1-2.so.3.gz
$sudo mv libstdc++-libc6.1-2.so.3 /usr/local/lib/
$sudo echo "/usr/local/lib" >> /etc/ld.so.conf
$sudo ldconfig
$./molekel4.3.linux