As can be seen below my first efforts were based on trying to install CueMol in a bona fide linux way, but that didn't work. However, a solution which definitely does work is:
1) Install Wine
2) Use Wine to install CueMol from the self-extracting Windows executable (it did work at this point, but the graphics window kept going blank as soon as the mouse was moved over one of the menu buttons or an atom was clicked on).
3) Install Lutris and use it to start CueMol. This will completely solve the dodgy graphics window problems.
Sadly, this solution is heavily reliant on the shoot-me-down gaming community, which slightly betrays my principles, but if you can't beat them...
[1] A google translation of this page on the CueMol web site.
Install dependencies
--------------------
Use the Synaptic Package Manager or 'sudo apt-get install' for the libraries mentioned on the above website plus libxt-dev.
Installing xulrunner
--------------------
Do as described in [1]
Get cuemol
----------
git clone https://github.com/CueMol/cuemol2.git cuemol2
Configure
---------
In /home/jon/cuemol2/uxbuild copy and paste the run_config_local_lxgui.sh script from the original Japanese i.e. untranslated page [1] since the translated one contains extra spaces and some of the -- have been converted to -.
sh run_config_local_lxgui.sh should produce the Makefile
make
make install
~/proj64/xulrunner-sdk/bin/xulrunner ~/proj64/cuemol2/src/xul_gui/application.ini
Sorry, this never worked in the end.
