<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="yiv8371825179"><div id="yui_3_16_0_1_1450204020471_24575"><div id="yui_3_16_0_1_1450204020471_24574" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div id="yiv8371825179"><div id="yiv8371825179yui_3_16_0_1_1450204020471_21488"><div id="yiv8371825179yui_3_16_0_1_1450204020471_21487" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div id="yiv8371825179yui_3_16_0_1_1450204020471_17987">Hi Pavel,</div><div dir="ltr" id="yiv8371825179yui_3_16_0_1_1450204020471_18045"><div dir="ltr" id="yiv8371825179yui_3_16_0_1_1450204020471_21511">I made a mistake with the output from phenix.reduce, now it works well. In my first attempt, the output from phenix.reduce was a file whose only content was: "USER MOD reduce.3.24.130724 H: found=0, std=0, add=0, rem=0, adj=0". It was solved when I renamed the input pdb. I took erroneously the first file as an input for phenix.refine and it produced an error (obviously). Now I repeated the refinement following exactly your instructions. I got the same results (as expected). </div></div><div id="yiv8371825179yui_3_16_0_1_1450204020471_17914"><span><br></span></div> <div class="" dir="ltr" id="yiv9530233138yui_3_16_0_1_1450197484812_7801">version:
dev-2247<br class="" id="yui_3_16_0_1_1450204020471_24618" clear="none">
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<div class="" dir="ltr" id="yiv9530233138yui_3_16_0_1_1450197484812_7735">Final: r_work = 0.1755 r_free = 0.2044 bonds = 0.030
angles = 0.598<br class="" id="yui_3_16_0_1_1450204020471_24622" clear="none">
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<div class="" dir="ltr" id="yiv9530233138yui_3_16_0_1_1450197484812_7686">version:
1.9-1692<br class="" id="yui_3_16_0_1_1450204020471_24625" clear="none">
</div>Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011
angles = 1.321<div class="yiv8371825179qtdSeparateBR" id="yiv8371825179yui_3_16_0_1_1450204020471_21547"><br clear="none"><br clear="none"></div><div class="yiv8371825179yqt4887124497" id="yiv8371825179yqt79444"></div></div></div></div><div class="yiv8371825179yqt1348819412" id="yiv8371825179yqt29314"><div id="yui_3_16_0_1_1450204020471_24605"> <div id="yui_3_16_0_1_1450204020471_24604" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div id="yui_3_16_0_1_1450204020471_24603" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div id="yui_3_16_0_1_1450204020471_24602" dir="ltr"><font id="yui_3_16_0_1_1450204020471_24601" face="Arial" size="2"> El Martes, 15 de diciembre, 2015 22:07:15, Pavel Afonine <pafonine@lbl.gov> escribió:<br clear="none"></font></div> <br clear="none"><br clear="none"> <div class="yiv8371825179y_msg_container"><div id="yiv8371825179"><div>
Hi Ezequiel<br clear="none">
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<div dir="ltr" id="yiv8371825179yui_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.
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"automatically add H's" in the phenix GUI uses phenix.reduce to add
H. The machinery that actually add H is exactly the same.<br clear="none">
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<div id="yiv8371825179yui_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;">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 clear="none">
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Does this create any problem?<div class="yiv8371825179yqt0254401083" id="yiv8371825179yqtfd47874"><br clear="none">
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Pavel<br clear="none">
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