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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: 972-8-647-2220��Skype:
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>
</div>
<div style="font-family: Times New Roman; color: #000000;
font-size: 16px">
<hr tabindex="-1">
<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>
</div>
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