Hello,<br><br>I&#39;m new to the world of x-ray crystallography.  I just solved my first SAD structure and I&#39;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&#39;m not sure if I&#39;m supposed to represent these residues as MET or MSE because it&#39;s a &quot;native,&quot; 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&#39;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&#39; and f&quot;, but it appears that nothing really changed.<br>

<br>Thanks!<br><br>Leigh Allen<br><br>*******<br>Ph.D Candidate<br>McCafferty Lab<br>Department of Chemistry<br>Duke University<br>