<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear All,<div><br></div><div>This is a question about the effect of solvent fraction estimation on the quality of the initial phases.</div><div>I am trying to solve the structure of a membrane protein at moderate resolution 3.5A from a MAD data set (peak, inflection and high energies). </div><div>I have one copy of my complex which gives me a solvent fraction of 0.7 without considering the contribution of the detergent.</div><div>With a related molecule I found a Phaser-MR solution but it does not refine although it is right. </div><div>I am using Phenix with the phases obtained from molecular replacement and combining them with the MAD signal to locate the seleniums. A visual inspection of the anomalous fourier difference map shows 6 sites out of the 7 expected at 4sigma contouring.</div><div><br></div><div>If I let Phenix decide by itself it goes on its own with two copies in the ASU and considers a solvent fraction of 0.50; then it finds 7 sites (and not 14 ? why is that?) (the seventh is weak but we expect this for this region of the complex).</div><div>now if I force Phenix to take ncs_copies=1 and solvent fraction=0.7 then it only find 6 sites.</div><div><br></div><div>Wether it is 2 "freely chosen" molecules/ASU and 0.5 of solvent or 1 "forced" molecule/ASU and 0.7 of solvent, the 6 first sites are identical (although occupancies are quite higher in the first case)</div><div>Should I take into account the detergent and lower somewhat my solvent fraction (in the 0.6 range maybe) with the fixed one copy ASU estimation or just trust Solve/Resolve when it runs the density modification part. Does it really affect the quality of the phasing? Between these two extremes I am surprised to see that the quality of the resolve map are quite similar apparently showing clear new structural features.</div><div><br></div><div><div><div>Thanks in advance for your comments,</div><div><br><br><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></div></div></div></body></html>