<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Peter,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>You are right. Somehow, the default target function in refinement.bulk_solvent_and_scale is LS, not ML. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Jianghai</DIV><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: 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; "><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; "><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; "><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; "><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; "><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; "><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; "><DIV>+++++++++++++++++++++++++++++++</DIV><DIV>Jianghai Zhu, Ph.D</DIV><DIV>CBR Institute for Biomedical Research</DIV><DIV>Department of Pathology</DIV><DIV>Harvard Medical School</DIV><DIV>200 Longwood Ave., Boston, MA 02115</DIV><DIV>Ph: 617-278-3211</DIV><DIV>Fx: 618-278-3232</DIV><DIV>+++++++++++++++++++++++++++++++</DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN> </DIV><BR><DIV><DIV>On Mar 25, 2007, at 8:18 PM, Petrus H Zwart wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><P>Hi Jianghai,</P><P>Interesting, I though that by default an ML target is used. Something must have happened somewhere.</P><P>Check the parameter file and look for the section on bulk solvent scaling ( refinement.bulk_solvent_and_scale ). A target function can be defined, you have the choice between ml and ls_wunit_k1, ml is (I think) selected by default.</P><P>There is also a switch present that triggers the refinement of bulk solvent parameters using a least squares target if the r value is larger than a certain value:</P><P>ls_bulk_solvent_and_scale_if_r_greater_then = 0.99</P><P>Changing the parameter you propose changes the least squares target type if the main target selected is ls and has (as far as I understand) no influence on bulk solvent scaling. If you want, you can send a log file for a closer look.</P><P>HTH</P><P>Peter</P><DIV> <BR class="khtml-block-placeholder"></DIV><DIV> <BR class="khtml-block-placeholder"></DIV><DIV> <BR class="khtml-block-placeholder"></DIV><P><BR><BR>----- Original Message ----- <BR>From: Jianghai Zhu <<A href="mailto:jzhu@cbr.med.harvard.edu">jzhu@cbr.med.harvard.edu</A>> <BR>Date: Sunday, March 25, 2007 2:58 pm <BR>Subject: [phenixbb] ls_wunit_k1 <BR>To: PHENIX user mailing list <<A href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</A>> <BR><BR>> Hi, <BR>> <BR>> I happen to notice that the target function of "Bulk solvent <BR>> correction and scaling" in a phenix.refine run is ls_wunit_k1. <BR>> Does <BR>> that mean LS function for bulk solvent correction and scaling is <BR>> the > default in phenix.refine? If I uncheck ls_wunit_k1 in <BR>> refinement.ls_target_names in my parameter file, will <BR>> phenix.refine <BR>> use the ML function or something bad will happen? <BR><BR>> <BR>> Jianghai <BR>> <BR>> +++++++++++++++++++++++++++++++ <BR>> Jianghai Zhu, Ph.D <BR>> CBR Institute for Biomedical Research <BR>> Department of Pathology <BR>> Harvard Medical School <BR> > 200 Longwood Ave., Boston, MA 02115 <BR>> Ph: 617-278-3211 <BR>> Fx: 618-278-3232 <BR>> +++++++++++++++++++++++++++++++ <BR>> <BR>> <BR>> <BR>> </P><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phenixbb mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>