Hi, The problem was that coot choked on the TER and BREAK lines in the PDB, once I removed these 0.4.1 reads the phenix PDBs fine. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I've just finished refinements with latest version of phenix (/phenix-1.3-final/build/mac-intel-osx/bin/phenix) in which I used riding hydrogens added with reduc (Molprobity) version and TLS - so I have anisou records - and a bunch of acs. When I open files in coot (coot/0.4.1/bin/coot) I see only 1 chain (I have a dimer chain A and B) and no solvent or other heteroatoms. The file displays fine in pymol - but I want to rebuild with coot. Any ideas ? I'm using the SBGrid install of coot, and a local installation of phenix. Thanks - Mark