<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">The bb bounced my email back because the enclosures were too big - let me know if you'd like them.<div><br></div><div>Thanks - </div><div><br></div><div>Miles</div><div><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="4" color="#000000" style="font: 14.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="4" style="font: 14.0px Helvetica">Miles Pufall <<a href="mailto:mpufall@cmp.ucsf.edu">mpufall@cmp.ucsf.edu</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="4" color="#000000" style="font: 14.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="4" style="font: 14.0px Helvetica">January 12, 2009 12:16:06 PM PST</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="4" color="#000000" style="font: 14.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="4" style="font: 14.0px Helvetica"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="4" color="#000000" style="font: 14.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="4" style="font: 14.0px Helvetica"><b>Refinement using new Phenix causes electron density/model mismatch</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Guys - <div><br></div><div>I am having a very puzzling problem using the new Phenix (1.4-3). I have about 20 structures that I am preparing to deposit with an accepted manuscript, and decided to do a final refine using the phenix.refine_gui not only to see if I got better numbers, but to use the integrated validation tools, which I love. Unfortunately, often, but not always, when I refine the pdb against the *_refine_data.mtz the statistics are a bit worse, and when I open the resulting *.map_coeffs.mtz in Coot it appears to be shifted with tons of negative electron density. Needless to say, this is making my nervous, so I've tried a few things:</div><div><br></div><div>1) Tried refining the same .pdb and .mtz files in Refmac - I seem to get the same shifting.</div><div>2) Try using the old .def file left over from the final run (just to make sure I didn't screw up some setting) - and I get the same shifting.</div><div>3) Try refining against the original .sca file - and I get the same shifting.</div><div>4) Try molecular replacement of the refined .pdb against the original .sca file - and sometimes, but not always, get a shift.</div><div><br></div><div>I am nervous and concerned - can you help me figure out what happened? I am enclosing an example - </div><div><br></div><div>refine_001.pdb = pdb I refined in new phenix</div><div>refine_001map_coeffs.mtz = mtz output from new phenix refinement (lots of red)</div><div>oste44a_output.sca = original scale file from HKL2000</div><div>MR.1_refine_data.mtz = data from which I am refining</div><div>sgk_ost_temp_H_refine_004.pdb</div><div><br></div><div>Thanks - </div><div><br></div><div>Miles</div><div></div></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><div><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><div>Miles Pufall</div><div>Postdoctoral Scholar</div><div>Yamamoto Lab</div><div>UC San Francisco</div><div>Cellular and Molecular Pharmacology</div><div>Mail Stop 2280</div><div>600 16th Street, Genentech Hall S-574</div><div>San Francisco, California 94158-2517</div><div>(415)476-4480</div><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><br class="Apple-interchange-newline"></span></div></span> </div><br></div></div></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><div>Miles Pufall</div><div>Postdoctoral Scholar</div><div>Yamamoto Lab</div><div>UC San Francisco</div><div>Cellular and Molecular Pharmacology</div><div>Mail Stop 2280</div><div>600 16th Street, Genentech Hall S-574</div><div>San Francisco, California 94158-2517</div><div>(415)476-4480</div><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><br class="Apple-interchange-newline"></span></div></span> </div><br></div></body></html>