- use Ralf's minimal covering sphere algorithm to pack everything together (Ralf: is it in svn?)

No. I found this to be a tricky problem. My implementation was just good enough for a specific purpose. I'm attaching the old script just in case it is useful as a starting point. Probably it doesn't run without modifications. It aims to move protein chains around minimizing the radius of the covering sphere. It isn't always what one would choose after visual inspection. The conformational search isn't exhaustive.
Ralf