<div dir="ltr"><div class="gmail_extra"><br><div class="gmail_quote">On 22 January 2013 10:03, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div id=":1g0">Hi Wolfram,<br>
<br>
each phenix.refine run creates a MTZ file that contains four sections of data:<br>
<br>
1) original data as supplied at input;<br>
2) data actually used in refinement (which may miss a few outliers, truncated by resolution and/or sigma if requested by the user, Fobs obtained from Iobs using French&Wilson method, etc);<br>
3) Fmodel: total model structure factors including all scales, etc. They can be used to reproduce reported R-factors exactly;<br>
4) Map coefficients: 2mFo-DFmodel (with and without filling missing Fobs), mFobs-DFmodel and anomalous difference map (f input data is anomalous: that is contains Fobs(+) and Fobs(-)).<br>
<br>
R-free flags are part of 1) and 2) above.<br>
<br>
That's the file that is supposed to go to PDB one way or another (as MTZ or CIF).<div class="yj6qo ajU"><div id=":1bc" class="ajR" tabindex="0"><img class="ajT" src="images/cleardot.gif"></div></div><span class="HOEnZb adL"><font color="#888888"><br>
<br>
Pavel</font></span><div class="HOEnZb adL"><div class="h5"><br>
<br>
On 1/22/13 9:28 AM, wtempel wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello all,<br>
based on ${prefix}_001_f_model.mtz from phenix.refine, I would like to<br>
prepare a cif file with structure factors.<br>
FOBS, SIGFOBS, R_FREE_FLAGS, FMODEL, PHIFMODEL, FOM are available in<br>
(+) and (-) versions, presumably representing Bijvoet pairs.<br>
My questions are:<br>
1) are FMODEL, PHIFMODEL the most appropriate columns for calculated<br>
amplitudes and phases for the purpose of PDB deposition?<br>
2) I understand that the PDB sf_tool does not accommodate separate<br>
(+)/(-) columns for some of the items. A job for<br>
phenix.reciprocal_space_arrays and a reflection file without anomalous<br>
differences?<br>
Alternatively, I imagine that phenix has a tailored procedure just for<br>
the preparation of PDB deposition, but I may not have used the correct<br>
web search terms to find the instructions.<br>
Thank you in anticipation,<br>
Wolfram Tempel<br>
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</div></div></div></blockquote></div><br>Hi Wolfram,</div><div class="gmail_extra"><br></div><div class="gmail_extra">You can use the option write_reflection_cif_file=True in phenix.refine to output an mmCIF reflection file that contains the same data as in the MTZ file as described by Pavel. I recently fixed a bug regarding output of anomalous arrays to the mmCIF file, so it would probably be best to try with the latest nightly build �The use of mmCIF for PDB deposition is an area we are actively working on right now, so we expect things to improve in this area in the near future.</div>
<div class="gmail_extra"><br></div><div class="gmail_extra">Cheers,</div><div class="gmail_extra"><br></div><div class="gmail_extra">Richard<br><br clear="all"><div><div>--</div><div><br></div><div>Richard Gildea</div><div>
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