<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yiv8040568168"><div id="yui_3_16_0_1_1450204020471_11531"><div id="yui_3_16_0_1_1450204020471_11530" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div id="yiv8040568168"><div id="yiv8040568168yui_3_16_0_1_1450204020471_7358"><div id="yiv8040568168yui_3_16_0_1_1450204020471_7357" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div id="yiv8040568168yui_3_16_0_1_1450204020471_4528">Hi Pavel</div><div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450204020471_4436"><div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450204020471_7369">phenix.reduce doesn't work well in my hands. I used "automatically add H's" in the phenix GUI instead. The other steps were exactly as you outlined (no water update). Thank you.</div></div><div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450204020471_4679"><br clear="none"></div><div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450204020471_4707">Ezequiel<br clear="none"></div><div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450204020471_4522">PS: phenix.reduce reads my file, but it output a pdb file with the added H's with "0" in the second column (and "new" in the last column)<br></div><div id="yiv8040568168yui_3_16_0_1_1450204020471_4349"><span></span></div> <br clear="none"><div class="yiv8040568168qtdSeparateBR" id="yiv8040568168yui_3_16_0_1_1450204020471_7365"><br clear="none"><br clear="none"></div><div class="yiv8040568168yqt3275738573" id="yiv8040568168yqt10082"></div></div></div></div><div class="yiv8040568168yqt2789334123" id="yiv8040568168yqt42971"><div id="yui_3_16_0_1_1450204020471_11694"> <div id="yui_3_16_0_1_1450204020471_11693" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div id="yui_3_16_0_1_1450204020471_11692" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div id="yui_3_16_0_1_1450204020471_11696" dir="ltr"><font id="yui_3_16_0_1_1450204020471_11695" face="Arial" size="2"> El Martes, 15 de diciembre, 2015 20:35:32, Pavel Afonine <pafonine@lbl.gov> escribió:<br clear="none"></font></div> <br clear="none"><br clear="none"> <div id="yui_3_16_0_1_1450204020471_11698" class="yiv8040568168y_msg_container"><div id="yiv8040568168"><div id="yui_3_16_0_1_1450204020471_11697">
Hi Ezequiel,<br clear="none">
<br clear="none">
version: dev-2247: Final: r_work = 0.1753 r_free = 0.2040<br clear="none">
vs <br clear="none">
version: dev-2247: Final: r_work = 0.1663 r_free = 0.2017<br clear="none">
<br clear="none">
look the same in a sense that if you 100 refinements each one
starting with a slightly perturbed model you will get 100 slightly
different refined models with both, Rwork and Rfree, varying withing
about 1% at this resolution. Having said that I can postulate that
r_work = 0.1753 is the same as r_work = 0.1663, and r_free = 0.2040
is the same as r_free = 0.2017.<br clear="none">
<br clear="none">
For some discussion see pages 75-77 here:<br clear="none">
<a rel="nofollow" shape="rect" class="yiv8040568168moz-txt-link-freetext" target="_blank" href="http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf">http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf</a><br clear="none">
and<br clear="none">
"Improved target weight optimization in phenix.refine" here:<br clear="none">
<a rel="nofollow" shape="rect" class="yiv8040568168moz-txt-link-freetext" target="_blank" href="http://phenix-online.org/newsletter/CCN_2011_07.pdf">http://phenix-online.org/newsletter/CCN_2011_07.pdf</a><br clear="none">
<br clear="none">
Now, before I proceed commenting, question: did you follow exactly
the steps 1)-2)-3) that I outlined in my previous email? Otherwise
it does not make much sense to compare results obtained using
different refinement settings.<br clear="none">
<br clear="none">
Pavel<br clear="none">
<br clear="none">
<br clear="none">
<div class="yiv8040568168yqt3277606339" id="yiv8040568168yqt38980"><div id="yui_3_16_0_1_1450204020471_11700" class="yiv8040568168moz-cite-prefix">On 12/15/15 12:00, Ezequiel Noguera
wrote:<br clear="none">
</div>
<blockquote id="yui_3_16_0_1_1450204020471_11702" type="cite">
<div id="yui_3_16_0_1_1450204020471_11701" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;">
<div id="yiv8040568168">
<div id="yiv8040568168yui_3_16_0_1_1450197484812_7406">
<div id="yiv8040568168yui_3_16_0_1_1450197484812_7405" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;">
<div id="yiv8040568168yui_3_16_0_1_1450133203464_3271">
<div id="yiv8040568168yui_3_16_0_1_1450197484812_7704">Thank you very
much, Pavel. I don't save H's when I modify the model
in coot (the input PDB file that I sent you was the
output from coot). I did the refinement again, now in
version 2247, without NCS. I got the same results,
higher R factors and RMS deviations for the newer
version. I got better results when I used "update
waters" (both in Rfactors and RMS). Below, I list the
statistics for refinement without updating waters.
Significant differences remain. Could it be any
difference in settings of default parameters between
versions?<br clear="none">
</div>
<div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450197484812_7801">version:
dev-2247<br clear="none">
</div>
<div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450197484812_7735">Start:
r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles =
1.321<br class="yiv8040568168" id="yiv8040568168yui_3_16_0_1_1450197484812_7799" clear="none">
Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030
angles = 0.593<br clear="none">
</div>
<div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450197484812_7686">version:
1.9-1692<br clear="none">
</div>
<div dir="ltr" id="yiv8040568168yui_3_16_0_1_1450197484812_7702">Start:
r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles =
1.409<br class="yiv8040568168" id="yiv8040568168yui_3_16_0_1_1450197484812_7685" clear="none">
Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011
angles = 1.321<br clear="none">
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote></div>
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