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<blockquote
cite="mid:875931344.523888.1420990260108.JavaMail.yahoo@jws106102.mail.bf1.yahoo.com"
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<div id="yui_3_16_0_1_1420691632447_454157" dir="ltr">1- after
getting structure refined with phenix.refine to �0.145 , 0.164
Rw/Rf. and then you feel happy with that.�</div>
<div id="yui_3_16_0_1_1420691632447_454157" dir="ltr">then after
using validation server from PDB you get�0.158 , 0.181 Rw/Rf.
why this big jump for R free. why phenix.refine giving us low
R free where in reality is not?</div>
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<br>
I would guess something happened to the model file.<br>
Can you reproduce R-factors yourself? Take data file and model that
you sent to PDB, and use either of availbale tools in Phenix to
compute R-factors:<br>
<br>
phenix.model_vs_data model.pdb data.mtz <br>
or<br>
phenix.refine model.pdb data.mtz strategy=none
main.number_of_macro_cycles=1<br>
<br>
Do you get the same R-factors?<br>
<br>
<blockquote
cite="mid:875931344.523888.1420990260108.JavaMail.yahoo@jws106102.mail.bf1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:16px">
<div id="yui_3_16_0_1_1420691632447_454157" dir="ltr">2- if i
want to show kick map for metal binding site for publication,
which map and how could i generate it.<br>
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<br>
Use FEM instead:<br>
<br>
phenix.fem model.pdb data.mtz<br>
<br>
There is option in the GUI too. More information<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/presentations/fem_06MAY2014.pdf">http://phenix-online.org/presentations/fem_06MAY2014.pdf</a><br>
<br>
Pavel<br>
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