Thanks to everyone who've replied to this thread. I really appreciated the help and the useful information. <div><br></div><div>Merry Xmas and Happy New Year everyone!! </div><div><br></div><div>Cheers</div><div>Da </div>
<div><br></div><div><br><div class="gmail_quote">On Fri, Dec 16, 2011 at 11:56 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 bgcolor="#FFFFFF" text="#000000">
I agree, it is a matter of convention. The total ADP is:
Utotal=Ucryst+Ugroup+Ulocal. You can either output the total Utotal
into ATOM/ANISOU records or keep Ucryst+Ugroup in REMARKs and output
Ulocal into ATOMs. Both ways are valid as long as they yield
identical Utotal. <br>
<br>
For more relevant information, summary and some review, see:<br>
<br>
- pages 23-29 here:<br>
<a href="http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf" target="_blank">http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf</a><br>
<br>
- article "On atomic displacement parameters (ADP) and their
parameterization in PHENIX" here:<br>
<a href="http://phenix-online.org/newsletter/" target="_blank">http://phenix-online.org/newsletter/</a><span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div><div class="h5"><br>
<br>
On 12/16/11 8:11 AM, Steiner, Roberto wrote:
<blockquote type="cite">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" target="_blank">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>
<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>
<div>
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</blockquote>
</div>
<br>
<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>
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