<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Da<div><br></div><div>Even if you deposit a structure refined with Refmac the PDB now expects the total B values being present. Have a look at</div><div><a href="http://deposit.rcsb.org/adit/REFMAC.html">http://deposit.rcsb.org/adit/REFMAC.html</a></div><div><br></div><div>What you call "more" correct does not really make much sense to me if I understand you properly. If you follow the link given above (or use TLSANL directly from the CCP4) and get 'total Bs' from Refmac I am sure they will be more or less the same and the Bs from phenix.refine. </div><div><br></div><div>R</div><div><br></div><div><br><div><div>On 16 Dec 2011, at 15:54, Da Duan wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Nat <br><br>I was just looking at the average B in the refinement log files from Refmac and Phenix Refine. Thanks for the clarification on how Refmac and Phenix calculate the average B. My next question is when depositing the structure, is it more common to deposit structures with the "residual" B-factors or B-factors generated by Phenix that includes the TLS and Ucryst contribution? I also performed sfcheck and the average B generated by the Wilson plot is ~100 which seems to suggest that the Phenix average B is probably "more" correct?<br>
<br>Thanks again <br><br>Da<br><br><br><br><div class="gmail_quote">On Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <<a href="mailto:2dd13@queensu.ca" target="_blank">2dd13@queensu.ca</a>> wrote:<br>
> I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of<br>
> rigidbody refinement with Phenix Refine I proceeded to restrained<br>
> refinement. The R/Rfree from the refinement decreased nicely as expected but<br>
> the B average is at ~100 (using Group B factor refinement option). I took<br>
> the same model and mtz through Refmac and the B average is about ~40. Has<br>
> anyone experienced this before? I am almost positive it maybe a setting<br>
> issue in Phenix Refine that i should be looking at to get the B factors to<br>
> refine correctly.<br>
<br>
</div>How are you calculating the average B? Refmac prints "residual"<br>
B-factors in the B column of ATOM records - these do not include the<br>
contribution from TLS and Ucryst (an overall B-factor for the entire<br>
crystal). In Phenix, the ATOM records always have the total isotropic<br>
B-factor, and this will always be higher than the equivalent in<br>
Refmac. So it's quite likely that both programs are correct, they're<br>
just reporting very different things. (And for what it's worth, a<br>
mean B-factor of 100 is totally normal at 3.3A resolution.)<br>
<br>
-Nat<br>
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<span><ATT00001..c></span></blockquote></div><br><div>
<div>Roberto Steiner, PhD</div><div>Randall Division of Cell and Molecular Biophysics Group Leader</div><div>King's College London</div><div><br></div><div>Room 3.10A </div><div>New Hunt's House </div><div>Guy's Campus</div><div>SE1 1UL, London, UK</div><div>Tel 0044-20-78488216</div><div>Fax 0044-20-78486435</div><div><a href="mailto:roberto.steiner@kcl.ac.uk">roberto.steiner@kcl.ac.uk</a></div><div><br></div><br class="Apple-interchange-newline">
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