<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">no, it just takes me two years to write up sometimes--- So this is a historical question. But there is a ref in that powerpoint to following ref. If this was implemented in Phenix and not Refmac 2 years ago, I should cite it.<div><br><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "></span></span></div><span class="Apple-style-span" style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 17px; "><div class="cit" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 0.8465em; font: inherit; vertical-align: baseline; line-height: 1.45em; "><a href="http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=robust%20bulk%20solvent%20correction#" title="Acta crystallographica. Section D, Biological crystallography." abstractlink="yes" alsec="jour" alterm="Acta Crystallogr D Biol Crystallogr." style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 11px; font: inherit; vertical-align: baseline; color: rgb(51, 51, 51); border-bottom-style: initial; border-bottom-color: initial; text-decoration: underline; ">Acta Crystallogr D Biol Crystallogr.</a> 2005 Jul;61(Pt 7):850-5. Epub 2005 Jun 24.</div><h1 style="margin-top: 0.375em; margin-right: 0px; margin-bottom: 0.375em; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 1.3846em; font: inherit; vertical-align: baseline; font-weight: bold; line-height: 1.125em; color: rgb(0, 0, 0); ">A <span class="highlight" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 18px; font: inherit; vertical-align: baseline; ">robust</span> <span class="highlight" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 18px; font: inherit; vertical-align: baseline; ">bulk</span>-<span class="highlight" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 18px; font: inherit; vertical-align: baseline; ">solvent</span> <span class="highlight" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 18px; font: inherit; vertical-align: baseline; ">correction</span> and anisotropic scaling procedure.</h1><div class="auths" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 0.923em; font: inherit; vertical-align: baseline; "><a href="http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Afonine%20PV%22%5BAuthor%5D" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 12px; font: inherit; vertical-align: baseline; color: rgb(51, 51, 51); border-bottom-style: initial; border-bottom-color: initial; text-decoration: underline; ">Afonine PV</a>, <a href="http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Grosse-Kunstleve%20RW%22%5BAuthor%5D" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 12px; font: inherit; vertical-align: baseline; color: rgb(51, 51, 51); border-bottom-style: initial; border-bottom-color: initial; text-decoration: underline; ">Grosse-Kunstleve RW</a>, <a href="http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Adams%20PD%22%5BAuthor%5D" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 12px; font: inherit; vertical-align: baseline; color: rgb(51, 51, 51); border-bottom-style: initial; border-bottom-color: initial; text-decoration: underline; ">Adams PD</a>.</div><div class="aff" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 0.8465em; font: inherit; vertical-align: baseline; line-height: 1.0915em; "><h3 class="label" style="margin-top: 1.2856em; margin-right: 1em; margin-bottom: 0.6428em; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 1.0769em; font: inherit; vertical-align: baseline; font-weight: bold; line-height: 1.2857; color: rgb(114, 65, 40); position: absolute; left: -10000px; top: auto; width: 1px; height: 1px; overflow-x: hidden; overflow-y: hidden; ">Source</h3><div style="margin-top: 0.5em; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 11px; font: inherit; vertical-align: baseline; ">Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA. <a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a></div></div><div class="abstr" style="margin-top: 1.2em; margin-right: auto; margin-bottom: auto; margin-left: auto; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; border-top-width: 0px; border-right-width: 0px; border-bottom-width: 0px; border-left-width: 0px; border-style: initial; border-color: initial; outline-width: 0px; outline-style: initial; outline-color: initial; font-size: 13px; font: inherit; vertical-align: baseline; "></div></span><div><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Arial; 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: Arial; 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>Tim</div><br class="Apple-interchange-newline"></span></span>
</div>
<br><div><div>On Apr 17, 2012, at 11:18 AM, Jeff Headd wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Tim,<div><br></div><div>If you are using Phenix 1.5.2, that would not have had the new bulk-solvent model that Pavel is talking about. Are you using that old of a version for your tests?</div><div><br></div><div>Jeff<br>
<br><div class="gmail_quote">On Tue, Apr 17, 2012 at 8:07 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi Tim,<br>
<br>
this is because recently (a few weeks ago) we introduced a novel
bulk-solvent model and a new overall anisotropic scaling procedure.<br>
<br>
Some detailed overview is here:<br>
<br>
<a href="http://www.phenix-online.org/presentations/PhenixSantaFe2012_PA.pdf" target="_blank">http://www.phenix-online.org/presentations/PhenixSantaFe2012_PA.pdf</a><br>
<br>
This is going to be published soon.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div><div class="h5"><br>
<br>
On 4/17/12 7:59 AM, Timothy Springer wrote:
<blockquote type="cite">In one of the structures I have refined, I found
phenix 1.5_2 gave 1 to 1.5% lower Rfree and Rwork than
<span style="font-size:12.0pt;font-family:"Times New Roman"">REFMAC
5.5.0102.</span> <br>
<div>Can I propose in a publication that "We <span>attribute these differences
to methods for handling bulk solvent in PHENIX that are less
adversely affected
by deficiencies in the crystallographic data."? </span></div>
<div><span>This is a guess, because there is a
large contribution to refinement from bulk solvent, rather
than factual information. I did cross-refinement, and found it
going from structures refined in REfmac to Phenix, and vice
versa. The Phenix maps looked better, too. </span></div>
<span>Is this a
reasonable suggestion, and would there be a relevant reference?<br>
</span>
<div>
<div style="font-size:12px">Tim<br>
</div>
</div>
</blockquote>
<br>
</div></div></div>
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