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Dear Tarek, not sure if I understood exactly what you wanted to ask.<br>
<br>
If you open the .mtz using a terminal/commandline with
phenix.mtz.dump -c yourmtz.mtz <br>
<br>
you will see the columns<br>
<br>
hkl F-obs SIF-obs R-free-flags <br>
<br>
and in the� R-free-flags colum you sometimes see a 0 or a 1. A 1
means that this reflection is flagged/marked as Rfree. A 0 that it
is used for refinement. Be aware that other programs might assign
different flag values. But when you than continue using phenix
refine it is usually clever enough to figure the right flag out.
Otherwise you can set the test flag value for phenix.refine in the
gui under configure --> input data --> test flag value<br>
<br>
At the end of the refinement just check in the result tab if #work
and #free are logical.<br>
<br>
Best Georg.<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 01/21/2015 11:05 PM, Tarek DawoD
wrote:<br>
</div>
<blockquote
cite="mid:2043487543.2843422.1421877937417.JavaMail.yahoo@jws10060.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:13px">
<div dir="ltr" id="yui_3_16_0_1_1421873316626_31729">Dear ALL</div>
<div dir="ltr" id="yui_3_16_0_1_1421873316626_31728"><br>
</div>
<div class="qtdSeparateBR"><br>
<br>
</div>
<div class="yahoo_quoted" id="yui_3_16_0_1_1421873316626_30996"
style="display: block;">
<div id="yui_3_16_0_1_1421873316626_30995">
<div id="yui_3_16_0_1_1421873316626_30994">
<div class="y_msg_container"
id="yui_3_16_0_1_1421873316626_30993">
<div id="yiv8970247139">
<div id="yui_3_16_0_1_1421873316626_30992">
<div style="background-color: rgb(255, 255, 255);"
id="yui_3_16_0_1_1421873316626_30991">
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><font
id="yiv8970247139yui_3_16_0_1_1421873316626_20054"
size="2">when you start you refinement in
phenix with ***.sca file, fraction of
reflection in test set will be created. under
<b>options </b>(bottom) in phenix refine, you
could see that�fraction of reflection in test
set is 0.1 which means 10 %</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><font
id="yiv8970247139yui_3_16_0_1_1421873316626_20069"
size="2">by looking to the PDB header for
completely different structures (below) you
will find different percentage but always�FREE
R VALUE TEST SET COUNT is around 3800. so it
always take the same 3800 count regardless the
number of reflections.</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><font
size="2"><br>
</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><font
id="yiv8970247139yui_3_16_0_1_1421873316626_20313"
size="2">When you look in generated mtz file
after the refinement, you see under
R-free-flags(+) and�R-free-flags(-) �either 0
or 1. what does 0 or 1 mean?</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><font
size="2"><br>
</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><font
id="yiv8970247139yui_3_16_0_1_1421873316626_20317"
size="2">Thank you in advance for explanation.</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><font
size="2"><br>
</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" dir="ltr" style="color:
rgb(0, 0, 0); font-family: HelveticaNeue,
'Helvetica Neue', Helvetica, Arial, 'Lucida
Grande', sans-serif;"><font
id="yui_3_16_0_1_1421873316626_31121" size="2">number
of reflection : 47312</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" dir="ltr" style="color:
rgb(0, 0, 0); font-family: HelveticaNeue,
'Helvetica Neue', Helvetica, Arial, 'Lucida
Grande', sans-serif;"><font
id="yui_3_16_0_1_1421873316626_31120" size="2">number
of reflections (non-anomalous): 24389</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" dir="ltr" style="color:
rgb(0, 0, 0); font-family: HelveticaNeue,
'Helvetica Neue', Helvetica, Arial, 'Lucida
Grande', sans-serif;"><font
id="yui_3_16_0_1_1421873316626_31112" size="2">R
value (working set): 0.1673</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" dir="ltr"><font
id="yui_3_16_0_1_1421873316626_31119" size="2">free
R value : 0.2084<br>
</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" dir="ltr"><font
id="yui_3_16_0_1_1421873316626_31124" size="2">free
r value test set size (%): 8.21</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" dir="ltr"><font
id="yui_3_16_0_1_1421873316626_31122" size="2">free
R value test set count : 3882</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" dir="ltr"><br>
</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" dir="ltr"><font
id="yui_3_16_0_1_1421873316626_31137" size="2">
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">number of
reflection : 107005</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">number of
reflections (non-anomalous): 56251</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">R value (working
set):0.1534�</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">free R value :
0.1997</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">free r value
test set size (%): 3.51</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">free R value
test set count : 3809</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style=""><br>
</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">number of
reflection : 48150</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">number of
reflections (non-anomalous): 25296</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">R value
(working set): 0.1470</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">free R value :
0.1918</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">free r value
test set size (%): 7.98</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style="">free R value
test set count : 3841</div>
</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style=""><br>
</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="" dir="ltr" style=""><br>
</div>
</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><font
id="yui_3_16_0_1_1421873316626_31405" size="2">TKDawoD</font></div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;" dir="ltr"><br>
</div>
<div
id="yiv8970247139yui_3_16_0_1_1421873316626_19750"
class="yiv8970247139" style="color: rgb(0, 0,
0); font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 8px;"><br
class="yiv8970247139" style="">
</div>
</div>
</div>
</div>
<br>
<br>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">
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