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">&lt;<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt;</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:&quot;Times New Roman&quot;">REFMAC
        5.5.0102.</span>  <br>
      <div>Can I propose in a publication that  &quot;We <span>attribute these differences
          to methods for handling bulk solvent in PHENIX that are less
          adversely affected
          by deficiencies in the crystallographic data.&quot;? </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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