suppose is a program for superimposing molecular structures and calculating RMSDs. It is written in the NAB language and is compiled for several popular architectures.
One of the main design goals was to be very flexible in the way atoms are selected used for both fitting structures and/or computing RMSDs. It makes pretty nice, consistent, easy to read output and is well documented in its html formatted man page. The actual source for the real man page lives at /sb/apps/man/man1/suppose.1. You can either put /sb/apps/man in your MANPATH environment variable or copy this file to somewhere that is already in your MANPATH. Then "man suppose" should get you going.
Contact Jarrod Smith if you have bug reports, questions or suggestions regarding suppose.