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Hi Jianghai,<br>
<br>
could you please send us .log file from your refinement run, so we can
analyze what's going on.<br>
<br>
In general, "bad" B-factors can be:<br>
- misplaced model;<br>
- inadequate TLS model (= domains chosen for TLS do not correspond to
the reality).<br>
<br>
If you are using like 2 months old or older version of phenix.refine,
you may want to get the latest CCI APPS since we made lots of
improvements. Just goto <a class="moz-txt-link-freetext" href="http://www.phenix-online.org/download/cci_apps/">http://www.phenix-online.org/download/cci_apps/</a><br>
<br>
Pavel.<br>
<br>
<br>
Jianghai Zhu wrote:
<blockquote
cite="mid1450356A-EEC5-48D2-9D05-C1DC3E7BD61A@cbr.med.harvard.edu"
type="cite">
<div><span class="Apple-style-span"
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<div>The resolution is 2.5 A. The wilson B is about 50. I know B
factor of the backbone is lower than that of the sidechian. But a B
factor like 4 is definitely wrong.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Jianghai</div>
<br class="Apple-interchange-newline">
</span></span></span></span></span></span></span> </div>
<br>
<div>
<div>On Dec 14, 2006, at 12:11 PM, Peter Zwart wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<blockquote type="cite">
<blockquote type="cite">
<div style="margin: 0px;">4) The refinement (TLS + ML + B
individual) went through, I got <span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">reasonable R, Rfree, rmsdBOND,
rmsdANGLE.<span class="Apple-converted-space"> </span>But the B
factors are <span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">pretty low.<span
class="Apple-converted-space"> </span>The B factor of the backbone
is much lower than the side <span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">chain, some have numbers like 4.<span
class="Apple-converted-space"> </span>Some metal atoms also have B <span
class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">factors around 4.<span
class="Apple-converted-space"> </span>What did I do wrong?</div>
</blockquote>
</blockquote>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">What is the resolution of your data?</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">Backbone B-s usually are lower than the
main chain.</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">What is the Wilson B value reported by
phenix.refine?</div>
<div style="margin: 0px;">You could re-refine and randomize all
B-values and see what happens (I<span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">have to get back to you to to get the
exact command for this). Maybe it<span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">is useful to obtain a copy of the latest
verison of phenix.refine by<span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">downloading cci_apps from our server <a
href="http://www.phenix-online.org">http://www.phenix-online.org</a>.</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">If your B-values still come out lowish,
try growing crystals that do not<span class="Apple-converted-space"> </span></div>
<div style="margin: 0px;">diffract very well, that usually does the
trick.</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">HTH</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">Peter</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
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</div>
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</div>
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</div>
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</div>
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</div>
<div style="margin: 0px; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">_______________________________________________</div>
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</blockquote>
</div>
<br>
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