<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Keitaro and Pavel,<div><br></div><div>thank you for your suggestions. I have now used the latest nightly build (1326). With this version, the average B-factor converges at about 52 A**2 and also the distribution is very similar, regardless with what B-factors I start the refinement (I tried average B-factors between 32 and 97). So clearly the behavior of this newest version is different from the version I have been using before (1.8.1 stable release 1168) and also from the latest stable release (1.8.2 stable release 1309), which behaves the same as 1168. To me the B-factors still look a bit too low, since the Wilson B-factor calculated by phenix is 66.45, the Wilson B-factor I determined manually from the linear part of the Wilson plot is 97.</div><div><br></div><div>Best regards</div><div><br></div><div>Florian</div><div><br></div><div><br><div><div>Am 19.03.2013 um 00:06 schrieb Keitaro Yamashita <<a href="mailto:yamashita@castor.sci.hokudai.ac.jp">yamashita@castor.sci.hokudai.ac.jp</a>>:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Florian,<br><br>Maybe you are using phenix-dev-1311 or earlier?<br>I am afraid that you have experienced the bug that overall B-factor is<br>not applied to individual atomic B-factors in certain cases, which I<br>have also experienced recently. That bug was fixed in dev-1312 if I<br>recall correctly.<br><br>Hope it helps,<br>Keitaro<br><br>2013/3/19 Florian Br�ckner <<a href="mailto:florian.brueckner@psi.ch">florian.brueckner@psi.ch</a>>:<br><blockquote type="cite">Dear all<br><br>I am refining a structure at 3.2 A with phenix.refine using automatic<br>optimization of target weights, solved by molecular replacement with a 2.1A<br>structure of the same crystal form. Rwork=26%, Rfree=28%. I use individual<br>atomic B-factor refinement. The obtained distribution of B-factors after<br>refinement looks reasonable and quite similar to the distribution in the<br>higher resolution model, which I suppose would be expected, since it is the<br>same crystal form. However, the average B-factor does not change<br>substantially, i.e. if I start with the B-factors from the high resolution<br>model (average B-factor around 32 A**2) after 6 macrocycles the average<br>B-factor is still around 32 A**2. If I set all B-factors to the Wilson<br>B-factor determined by phenix.refine (66 A**2), after 6 macrocycles the<br>distribution of B-factors looks again very similar to the high resolution MR<br>model, but the average B-factor is still around 65 A**2. What should I make<br>of this? Is this an expected behavior at this resolution, i.e. the fact that<br>the absolute values of B-factors cannot be determined during refinement,<br>although a reasonable distribution can be obtained as judged by plotting<br>average B-factors vs. residue#? Since the average B-factor does not change<br>much during refinement, which average B-factor should I start refinement<br>with to end up with reasonable absolute values? I have manually determined<br>the Wilson B-factor from the linear part of the Wilson plot (4.5-3.2 A) to<br>be 97 A**2. This seems high to me. Would that be expected for the given<br>resolution, given that the 2.1A structure of the same crystal form has 32<br>A**2? I should add, that there is not a substantial effect of the average<br>refined B-factor on Rfree.<br><br>Thanks for any comments or suggestions.<br><br>Best regards<br><br>Florian<br><br><br>-------------------------------------------------------------<br><br>Dr. Florian Br�ckner<br>Laboratory of Biomolecular Research (LBR)<br>OFLG/102<br>Paul Scherrer Institut<br>CH-5232 Villigen PSI<br>Switzerland<br><br>Tel.: +41-(0)56-310-2332<br>Email: <a href="mailto:florian.brueckner@psi.ch">florian.brueckner@psi.ch</a><br><br><br><br><br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br><br></blockquote>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">-------------------------------------------------------------</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; ">Dr. Florian Br�ckner<br>Laboratory of Biomolecular Research (LBR)</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">OFLG/102<br>Paul Scherrer Institut<br>CH-5232 Villigen PSI<br>Switzerland<br><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Tel.:<span class="Apple-tab-span" style="white-space: pre; "> </span>+41-(0)56-310-2332<br>Email:<span class="Apple-converted-space"> </span><span class="Apple-tab-span" style="white-space: pre; "> </span><a href="mailto:florian.brueckner@psi.ch">florian.brueckner@psi.ch</a><br><br><br><br></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span>
</div>
<br></div></body></html>