Hello, I've recently used--for the first time--phenix's ligand_identification tool via the GUI, and am now examining the output files. I'm writing to ask for advice on how to view the map and models using Coot. I could open the 'model_RSR_FITTED_###.pdb' file with PyMOL, and I could inspect where in the model the fit ligand sits, but I prefer to look at the map using Coot. At this point I have two problems: First, when I Auto Open the resolve.mtz file in Coot, the model I'd input to ligand_identification is clearly not aligned with the map. What could have happened here? And how might I fix it? Second, the same 'model_RSR_FITTED_###.pdb' file I opened with PyMOL has in Coot just one chain, and that contains only the fit ligand. Thanks in advance for any input, Emily Arturo Ph.D. program in Biochemistry, Drexel Univ College of Medicine Jaffe lab, Fox Chase Cancer Center Philadelphia, PA