The question: "I've fitted (successfully !!!) two objects using lsq_explicit, applied the tranformation (another success) and I'm happy, but... when I quit the session the objects revert back to the untransformed ones (as could be expected, I suppose). Is there a clever/simple way of keeping the object in the transformed form from session to session ?"
Alwyn explained: "there is no data structure in o that knows about transformations applied to objects. in the next MAJOR release (6.0) this will be added. for now, you should use a macro to apply all transformations to objects. 4d users have the additional problem of being unable to ID atoms in transformed molecular objects (for the above reason)"
Pete Dunten helped out: "You can also do lsq_mol (manual section 3.8.4) after making a copy of your molecule's coordinates. That way you will have both the original and the transformed copies available to look at/pick atoms/etc. See also rot_trans_db (manual section 3.20.1) for the more general case."
Mark Saper hinted: "I use the determined transformation with the Merge_atoms command. This command is very handy since it allows you to apply transformations to residues and copy them to some other place, even in the same molecule."