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<div style="direction: ltr;font-family: Arial;color: #0000FF;font-size: 10pt;">Hi Pavel,<br>
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<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>
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<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>
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<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.
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<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>
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<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>
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<div style="font-family:Tahoma; font-size:13px"><font size="3" face="Arial"> Boaz<br>
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<div><font color="#000080" size="3" face="Times New Roman"><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: bshaanan@bgu.ac.il<br>
Phone: 972-8-647-2220 Skype: boaz.shaanan <br>
Fax: 972-8-647-2992 or 972-8-646-1710 </em></font></div>
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<div id="divRpF114326" style="direction: ltr;"><font color="#000000" size="2" face="Tahoma"><b>From:</b> Pavel Afonine [pafonine@lbl.gov]<br>
<b>Sent:</b> Tuesday, November 07, 2017 10:39 PM<br>
<b>To:</b> ��� ����; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: Question about writing cif files at the last round of refinement<br>
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<div>Hi Boaz,<br>
<br>
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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>
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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>
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CIF with reflections contains these fields:<br>
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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>
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where F_meas_au is a name for Fobs (clearly, a weird way to name Fobs, not sure who invented it!).<br>
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This is what I get myself using the latest code. Is it different for you?<br>
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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>
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