CHAINis a somewhat distant decendent of
FRODO, and while one of the more user-friendly of the electron density fitting packages, it is no longer actively being developed and supported by F. Quiocho's group at Baylor. While what we have works just fine, if you are going to be doing more than studying mutants and ligand complexes, it might be worth your while to learn 'O'. The documentation, while complete, is nearly impossible to comprehend in its organization. I prefer to use it 'on-line' and use text-searches to find what I need, since the information you are looking for probably won't be where you think it should be!
A new version of
CHAIN (7.1) can be made available to you if you are interested, however it is a fairly major departure from previous versions and it is not entirely compatible with previous session files, et cetera. I have produced an HTML version of the new manual which is a considerable improvement over the previous forms of the documentation.