>Does anybody know about a command line orientated tool for superimposing
>protein structures on Linux? For the superimposition I'd like to use not
>only c-alpha atoms but also any type of atom pairs.
ProFit from Andrew Martin http://www.bioinf.org.uk/
VMD (code I once worked on) can do some of this as well
(it's a visualization program but doesn't need to run with a GUI)
dalke at dalkescientific.com