Hello Rex,
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.
Pavel