This is a beta copy of LoopTool. It is intended to be used with Zuker's RNA folding software to be released later. Use this at your own risk. The documentation is limited to the LoopTool.help file which should go in your GDE_HELP_DIR. 1. Copy LoopTool into your binary directory with all of the other GDE programs. 2. Edit the .GDEmenus file in the $GDE_HELP_DIR directory. Remove the old "Show Secondary structure" item, up to the next line starting with "item:". Then insert the contents of GDEmenus_addition into the same place in your .GDEmenus file. 3. Copy the file LoopTool.help into the $GDE_HELP_DIR directory. 4. Inform all people using their own local .GDEmenus files that there has been a change, and that they may wish to update their copy. You should then be able to run gde on the demo file HelixExampletRNAs to display the structure. Good luck, Steve