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Could you please send me the entire set of inputs and outputs for
this refinement run (using dev-2247)? Please send files off-list. <br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/15/15 16:17, Ezequiel Noguera
wrote:<br>
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<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: "USERÂ 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>
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<div
id="yiv8371825179yui_3_16_0_1_1450204020471_17914"><span><br>
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<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">
</div>
<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
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<div id="yui_3_16_0_1_1450204020471_24602"
dir="ltr"><font
id="yui_3_16_0_1_1450204020471_24601" size="2"
face="Arial"> El Martes, 15 de diciembre, 2015
22:07:15, Pavel Afonine
<a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a> escribió:<br
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<div> Hi Ezequiel<br clear="none">
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id="yiv8371825179yui_3_16_0_1_1450204020471_11531">
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<div
id="yiv8371825179yui_3_16_0_1_1450204020471_7358">
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id="yiv8371825179yui_3_16_0_1_1450204020471_7357"
style="color:#000;background-color:#fff;font-family:HelveticaNeue,
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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. </div>
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<br clear="none">
"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
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id="yiv8371825179yui_3_16_0_1_1450204020471_11531">
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id="yiv8371825179yui_3_16_0_1_1450204020471_11530"
style="color:#000;background-color:#fff;font-family:HelveticaNeue,
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<div
id="yiv8371825179yui_3_16_0_1_1450204020471_7358">
<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
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Does this create any problem?
<div class="yiv8371825179yqt0254401083"
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Pavel<br clear="none">
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