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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 --&gt; input data --&gt; 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>
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      <br>
      <pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">
</pre>
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