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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