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    <font color="#000000">Hi Boaz,<br>
      <br>
      hm.. this odd. I'm using developers version which is close to
      latest nightly build.<br>
      <br>
      Before I ask for all inputs that reproduce this problem, could you
      please do this quick and simple test? Step-by-step:<br>
      <br>
      1) Get model and data:<br>
      <br>
      phenix.fetch_pdb 1yjp --mtz<br>
      <br>
      2) Start Phenix GUI, then run refinement using 1yjp.mtz and
      1yjp.pdb files, do not change any settings except for </font><font
      color="#000000">"Write final refined model into mmCIF file" and
      "Write Fobs, Fmodel and R-free-flags into mmCIF file" being enabled.<br>
      <br>
      This is what I did and I'm getting reflection CIF file with Fobs
      included.<br>
      <br>
      Thanks,<br>
      Pavel<br>
      <br>
    </font><br>
    <div class="moz-cite-prefix">On 11/7/17 13:24, Boaz Shaanan wrote:<br>
    </div>
    <blockquote type="cite"
cite="mid:4B2A491F685D1E4FBBF985E193095AAF012F4E78B1@hawk3.auth.ad.bgu.ac.il">
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      <div style="direction: ltr;font-family: Arial;color:
        #0000FF;font-size: 10pt;">Hi Pavel,<br>
        <br>
        <font size="4">Thanks for your message. I did tick two boxes (as
          also evidenced from checking the final.eff. Here is what I
          get:<br>
          <br>
        </font>
        <div><font size="4">loop_<br>
             _refln.index_h<br>
             _refln.index_k<br>
             _refln.index_l<br>
             _refln.pdbx_FWT<br>
             _refln.pdbx_PHWT<br>
             _refln.pdbx_DELFWT<br>
             _refln.pdbx_DELPHWT<br>
             _refln.pdbx_r_free_flag<br>
             _refln.status<br>
             _refln.pdbx_F_calc_with_solvent<br>
             _refln.pdbx_phase_calc_with_solvent<br>
            <font size="3"><br>
            </font></font>
          <div style="font-family:Tahoma; font-size:13px">
            <div><font size="3">So it seems as if the first two items in
                your list: _refln.F_meas_au AND _refln.F_meas_sigma_au
                (which is what I was looking for, that is Fobs and
                Sigfobs) are missing.
                <br>
              </font></div>
            <div><font size="3">What version are you running? I'm
                running phenix-dev-2919 (I tried 2949, the latest bild
                as of yesterday, and it failed altogether to start a
                refinement cycle; I reported it to bugs@...).</font></div>
            <font size="3">I'll have a look again on the download site.</font></div>
          <div style="font-family:Tahoma; font-size:13px"><font size="3"><br>
            </font></div>
          <div style="font-family:Tahoma; font-size:13px"><font size="3"
              face="Arial">Thanks for pointing out the problem with
              mmtbx.prepare_pdb_deposition</font></div>
          <div style="font-family:Tahoma; font-size:13px"><font size="3"
              face="Arial"><br>
            </font></div>
          <div style="font-family:Tahoma; font-size:13px"><font size="3"
              face="Arial">Boaz<br>
            </font>
            <div><font size="3"></font></div>
            <div><font size="3" face="Times New Roman" color="#000080"><em>Boaz
                  Shaanan, Ph.D.
                  <br>
                  Dept. of Life
                  Sciences <br>
                  Ben-Gurion University of the
                  Negev <br>
                  Beer-Sheva
                  84105 <br>
Israel <br>
 <br>
                  E-mail: <a class="moz-txt-link-abbreviated" href="mailto:bshaanan@bgu.ac.il">bshaanan@bgu.ac.il</a><br>
                  Phone: 972-8-647-2220Skype:
                  boaz.shaanan <br>
                  Fax: 972-8-647-2992 or 972-8-646-1710</em></font></div>
            <div><font size="3" face="Times New Roman" color="#000080"><em></em></font></div>
            <div><font size="3" face="Times New Roman" color="#000080"><em></em></font></div>
            <div><font size="3" face="Times New Roman"><em><font
                    color="#000080">
                    <br>
                    <br>
                  </font></em></font></div>
          </div>
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          <div id="divRpF114326" style="direction: ltr;"><font size="2"
              face="Tahoma" color="#000000"><b>From:</b> Pavel Afonine
              [<a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>]<br>
              <b>Sent:</b> Tuesday, November 07, 2017 10:39 PM<br>
              <b>To:</b>  ; <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
              <b>Subject:</b> Re: Question about writing cif files at
              the last round of refinement<br>
            </font><br>
          </div>
          <div>Hi Boaz,<br>
            <br>
            <blockquote type="cite">
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              <div style="direction:ltr; font-family:Arial;
                color:#0000FF; font-size:10pt"><font size="2"
                  face="Times New Roman">Perhaps I'm doing something
                  wrong but it seems as if I follow the instructions
                  correctly. To write cif files (data and model) in the
                  final refinement run I tick the correct boxes in the
                  output box of the gui. I can see in the final.eff that
                  this was accepted. However the data cif file contains
                  only the model derived quantities and not the original
                  Fobs, sigFobs etc. as they are on incoming mtz file.
                  In the next stage, as you
                  propose,mmtbx.prepare_pdb_deposition routine expects
                  those quantities (i.e. Fobs etc.). I'm running the
                  nightly build 2919. Am I doing something wrong? I'd
                  appreciate your advice.</font></div>
            </blockquote>
            <br>
            first, you should tick two boxes: "Write final refined model
            into mmCIF file" and "Write Fobs, Fmodel and R-free-flags
            into mmCIF file". Then after refinement you should get two
            CIF files *_refine_*.cif (refined model) and
            *_refine_*.reflections.cif (reflections).<br>
            <br>
            CIF with reflections contains these fields:<br>
            <br>
            loop_<br>
             _refln.index_h<br>
             _refln.index_k<br>
             _refln.index_l<br>
             _refln.F_meas_au<br>
             _refln.F_meas_sigma_au<br>
             _refln.pdbx_FWT<br>
             _refln.pdbx_PHWT<br>
             _refln.pdbx_DELFWT<br>
             _refln.pdbx_DELPHWT<br>
             _refln.pdbx_r_free_flag<br>
             _refln.status<br>
             _refln.pdbx_F_calc_with_solvent<br>
             _refln.pdbx_phase_calc_with_solvent<br>
            <br>
            where F_meas_au is a name for Fobs (clearly, a weird way to
            name Fobs, not sure who invented it!).<br>
            <br>
            This is what I get myself using the latest code. Is it
            different for you?<br>
            <br>
            mmtbx.prepare_pdb_deposition seems to broken: I just ran a
            sample example where I asked to output model and reflection
            CIFs, and then supplied them to mmtbx.prepare_pdb_deposition
            and it crashed. Also, it crashes if I give it PDB and MTZ
            from refinement.<br>
            <br>
            Pavel<br>
            <br>
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