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nihmmayerm wrote: > 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. Hmm... where, I suspect, "choked on" means "parse according to the definition". I have not heard before of a BREAK card and AFAICS, it is not part of the 2.3 standard - so I am not surprised that Coot does not parse your file in the way you might expect. Paul.