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<p>Dear Pavel,</p>
<p>I agree with every single one of your points. As I mentioned, it
is not phenix.refine that reports a cutoff, but the Protein Data
Bank. My point was to have the Protein Data Bank record correctly
what phenix.refine provides, and prevent confusion (as was the
case for the original post). The "wishful thinking" you have
pointed out is being done by the PDB on every single
phenix-generated structure, so I hope that they change this
practice if they see this post.<br>
</p>
<p>I understand that PHENIX developers cannot be responsible for
what third parties, such as the Protein Data Bank, do with files
provided by your software.<br>
</p>
<p>Thank you for the awesome software,</p>
<p>Engin<br>
</p>
<br>
<div class="moz-cite-prefix">On 1/8/18 10:35 AM, Pavel Afonine
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:e7cca8be-bff0-bc20-d05e-22122ff10c14@lbl.gov">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Hi Engin,<br>
<br>
thanks for feedback!<br>
<br>
<blockquote type="cite"
cite="mid:08bcc65f-8318-6642-a3af-87ea7cce26fe@uchicago.edu">There
is one complication that arises from the report of the
MIN(FOBS/SIGMA_FOBS) value in pdb files from phenix.refine.
Nearly every PDB entry using phenix.refine reports a F/sig(F)
cutoff value of 1.3x, </blockquote>
<br>
As I eluded yesterday, this is not a cutoff but a reported fact
about your data. No data is removed or otherwise manipulated
related to this number. <br>
<br>
<blockquote type="cite"
cite="mid:08bcc65f-8318-6642-a3af-87ea7cce26fe@uchicago.edu">while
Buster and Refmac-generated pdbs have 0 or -/None for that value
(just checked again with this week's released PDBs). This is
clearly not intended. Again, the value the Protein Data Bank is
reporting is a cutoff, based on the minimum value phenix.refine
appears to report. Since I use French-Wilson for I to F
conversions, I have had to correct this cutoff value by
communicating with PDB with every deposition, but it appears
that most users rarely go through the trouble. <br>
</blockquote>
<br>
REMARK 3 records are free format. It's up to program authors to
choose what to print there.<br>
<br>
Nowhere in the record in question produced by phenix.refine is
said "cutoff":<br>
<pre style="color: rgb(0, 0, 0); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial; word-wrap: break-word; white-space: pre-wrap;">REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380
</pre>
Refmac and Buster print:<br>
<pre style="color: rgb(0, 0, 0); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial; word-wrap: break-word; white-space: pre-wrap;">REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
</pre>
which clearly says "cutoff".<br>
<br>
So I guess we are fine as long as there is no wishful thinking
involved and people carefully read what's written!<br>
<br>
<blockquote type="cite"
cite="mid:08bcc65f-8318-6642-a3af-87ea7cce26fe@uchicago.edu">
The issue seems to arise from a lack of a cutoff value in the
phenix.refine generated .pdb files; Refmac has a DATA CUTOFF
(SIGMA(F)) (set to NONE by default), which is picked up during
structure deposition. So, either PDB has to be told that
phenix.refine min value is just a minumum value and not a
cutoff, or phenix.refine might add another REMARK card for DATA
CUTOFF (SIGMA(F)) under the DATA USED IN REFINEMENT. section in
REMARKS.<br>
</blockquote>
<br>
Sure, we can add "cutoff"record if you think it is helpful.<br>
<br>
In general, there are way more facts to reports about the data
than this single number. As long as people deposit 1) data
actually used in refinement (that may be truncated by sigma,
resolution, automated outlier rejection, Iobs converted to Fobs,
anomalous F+/- converted to non-anomalous Imean, etc) and 2)
original data (not manipulated in any way), and as long as PDB
actually accepts these data, then all should be fine. Note:
phenix.refine always outputs MTZ containing the original input
data and data actually used in refinement.<br>
<br>
All the best,<br>
Pavel<br>
<br>
</blockquote>
<br>
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