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<div>Dear All,</div><div>I am trying to refine a seleno met structures at 2.2 Ang resolution</div><div>I used Auto_Sol and Auto_Build and it worked great since it found the 4 semets with occupancies of about 0.85 to 0.95. and most of the model was built. Phenix generated an exptl_fp_phases.mtz with the Rfree flag. so far so good. I have a couple of questions because I am not quite to understand what phenix.refine is doing at this stage?</div><div>1- If I refine using the experimental phases mtz file generated by the auto_sol run, the occupancies for the seleniums change quite a bit and they drop to 0.75-0.80 and that does not sound right to me? What am I doing wrong? should I fix occupancies for the seleniums to the values evaluated at the end of the auto_build run (Rfree=27/ Rfac=24?)</div><div>2- This experimental phases mtz file contains FP and the HL coefficients for the phases but there are no more anomalous differences. If I try to refine f' and f" using it, Phenix tells me that there is no anomalous information contained in this file. So how do you refine f' and f"? and what is the practical reason for this AutoSol generated mtz file to not contain the anomalous differences that were used to locate the seleniums. </div><div><br></div><div>Thanks in advance for the explanation</div><div><br></div><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div><div>Pascal F. Egea, PhD</div><div>Post Doctoral Researcher</div><div>University of California San Francisco</div><div>Department of Biophysics and Biochemistry</div><div>Robert Stroud Laboratory</div><div><a href="mailto:pascal@msg.ucsf.edu">pascal@msg.ucsf.edu</a></div></div></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"> </div><br></body></html>