<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">I consider you guys have done an excellent job. I am just curious for the things happened during my refinement.<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 26, 2007, at 11:42 AM, Petrus H Zwart wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><P>I guess that development time is a factor that one should take into consideration when seeing these issues. The phenix release that we currently have is still alpha !</P><P>The program is not as mature as other refinement programs, but gives good results across the board. phenix is still a work in progress...</P><P>P</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: Monday, March 26, 2007 6:14 am <BR>Subject: Re: [phenixbb] ls_wunit_k1 <BR>To: PHENIX user mailing list <<A href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</A>> <BR><BR>> I found the "automatic adjustment" in my log file. It says that <BR>> the <BR>> target for bulk solvent correction and scaling is changed to <BR>> ls_wunit_k1 and is required for the target mlhl. Why is that? <BR>> for <BR>> stability issues? <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> > On Mar 26, 2007, at 12:41 AM, Ralf W. Grosse-Kunstleve wrote: <BR>> <BR>> >> All right. The target for my TLS is also LS. Is that <BR>> intentional <BR>> >> too? <BR>> > <BR>> > Pavel, who wrote the TLS code, is current offline. <BR>> > <BR>> > I don't know if Pavel ran systematic tests to determine the default <BR>> > target for TLS. <BR>> > <BR>> > A couple of months ago I ran systematic tests exercising rigid body <BR>> > refinement using both the LS and ML targets. Overall it turned <BR>> out <BR>> > that <BR>> > ML is slightly better than LS. For an individual structure and a <BR>> > particular starting point it can be the other way around, but <BR>> averaged> over about 70 structures with 100 random starting points <BR>> each ML <BR>> > generally outperforms LS. We should have updated the default <BR> > > accordingly, but it fell through the cracks. <BR>> > <BR>> > If you have the time to try out both ML and LS in the refinement of <BR>> > your structure, we'd be interested to know the results. <BR>> > <BR>> > Ralf <BR>> > <BR>> > P.S.: What's the version of phenix.refine you are using? -- I'm <BR>> still> puzzled why you didn't get the "automatic adjustment" messages. <BR>> > _______________________________________________ <BR>> > phenixbb mailing list <BR>> > <A href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</A> <BR>> > <A href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</A> <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>