Hello, I'm new to the world of x-ray crystallography. I just solved my first SAD structure and I'm on to the refinement stage. The difference map generated by phenix.refine has really big positive peaks all around my MET residues. If I switch the atoms to MSE, then I get large negative peaks. Firstly, I'm not sure if I'm supposed to represent these residues as MET or MSE because it's a "native," high resolution (1.85) dataset, but it the protein had MSE residues. When scaling this data, I did not keep F(+) and F(-) separate. The protein's phases were generated using SAD data to 2.7A, which using SHARP led to a remarkably interpretable map that allowed me to build in the protein by hand. My second question is, how should I handle the issue with large + MET/large - MSE peaks? Do I need to rescale my data to treat it as anomalous data or is there something I can do within Phenix to fix my problem. I tried the phenix.refine GUI and set it up to refine f' and f", but it appears that nothing really changed. Thanks! Leigh Allen ******* Ph.D Candidate McCafferty Lab Department of Chemistry Duke University