Can I read a Shelx file with Phenix and
output the new pdb in Phenix format?
no, sorry. Shelx format isn't really well supported. We have some
code that can parse these files but I have no idea how up-to-date it
is and I doubt it is very well tested, and it is not user-level
exposed.
Only PDB and mmCIF are fully supported in most tools (Tom, Randy: is
mmCIF supported in Phaser and Autobuil and other related
utilities?).
I guess you can convert Shelx file into PDB file with dedicated
Shelx utility (ShelxPro?). I would expect Tim can offer more
comments.