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Hi,<br>
<br>
many thanks for this go to Ezra Peisach who was extremely helpful in
addressing this problem at the RCSB end, and Mischa of course too,
who reported the problem and fearlessly shared the data!<br>
<br>
All the best,<br>
Pavel<br>
<br>
On 12/20/11 12:26 PM, Machius, Mischa Christian wrote:
<blockquote
cite="mid:D05D29DF-12E5-4EC8-873E-1E3290417E87@ad.unc.edu"
type="cite">
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charset=ISO-8859-1">
Y'all,
<div><br>
</div>
<div>Thanks for your comments, suggestions and empathy.</div>
<div><br>
</div>
<div>It turns out that there was a bug in the structure factor
conversion program that the PDB uses. The phenix mtz file is
just fine. Everything appears to be in working order, and nobody
should run into the same issue from now on. </div>
<div><br>
</div>
<div>Cheers!</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>On Dec 16, 2011, at 10:03 AM, Felix Frolow wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
Misha, you will be surprised how many times people were in
situations similar to yours with PDB or PDB-EBI.
<div>Myself was not able to submit data after PHENIX
refinement, as I ALWAYS separate between anomalous + and
- reflections</div>
<div>during refinement. PHENIX provides I(+) and I(-) for
submission (in my case as I never you F's for
refinement, only I's) but not I average, PDB-EBI refuses
to accept such data</div>
<div>and PHENIX refuses to provide redundant information. </div>
<div>The end is that one need to re-refine using
diffraction data presentation formalism which PDB will
accept in order </div>
<div>not to provide data that was not used for refinement
but was chosen for submission convenience.<br>
<div apple-content-edited="true"><span
class="Apple-style-span" style="border-collapse:
separate; font-family: Helvetica; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto; text-indent:
0px; text-transform: none; white-space: normal;
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-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; font-size: medium; ">Dr
Felix Frolow <br>
Professor of Structural Biology and Biotechnology<br>
Department of Molecular Microbiology<br>
and Biotechnology<br>
Tel Aviv University 69978, Israel<br>
<br>
Acta Crystallographica F, co-editor<br>
<br>
e-mail: <a moz-do-not-send="true"
href="mailto:mbfrolow@post.tau.ac.il">mbfrolow@post.tau.ac.il</a><br>
Tel: ++972-3640-8723<br>
Fax: ++972-3640-9407<br>
Cellular: 0547 459 608</span> </div>
<br>
<div>
<div>On Dec 16, 2011, at 16:50 , Machius, Mischa
Christian wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Robbie,<br>
<br>
Yes, the thought that the anomalous R free flags
could have something to do with it occurred to me
as well, so I checked. As far as I can see, the
test reflections are evenly distributed between
the + and - sets; they were not selected from the
+ or - set only. For the vast majority of the test
reflections, both Bijvoet mates were measured and
both were flagged properly. For some, however,
only one Bijvoet mate was measured and flagged. It
probably wouldn't do any harm to consolidate the
test flags, discarding the few with only one
measured Bijvoet mate, but I really don't see why
it should be necessary to do so.<br>
<br>
For now, I have converted the reflection file into
the CNS format and sent to the PDB, hoping that
they will be able to deal with that one properly.
<br>
<br>
Bit surprised though that no one has run into that
problem before.<br>
<br>
Thanks for your suggestion.<br>
<br>
MM<br>
<br>
<br>
On Dec 16, 2011, at 3:54 AM, Robbie P. Joosten
wrote:<br>
<br>
<blockquote type="cite">Hi Mischa,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Your mtz file seems to
contain 'anomalous' free R-flags (that is what I
gather from Pavel's post). This is kind of
weird. Do you really want I+ in the work set and
I- in the test set? That would bias your R-free.
If the two flags match (which I really hope),
then you can leave one column out before you
(re)deposit your data. This will hopefully
solves the problem.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Cheers,<br>
</blockquote>
<blockquote type="cite">Robbie Joosten<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Netherlands Cancer
Institute<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">On 12/15/2011 05:40 PM,
Machius, Mischa Christian wrote:<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Y'all,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">While depositing a
structure, the PDB 'complained' about my
structure-factor file, saying they don't
contain R-free flags or are otherwise
incomplete. The comment was prompted by their
Refmac R-factor test failing.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">The structure-factor
file I submitted came from phenix.refine
(xxx_data.mtz). I am using version 1.7.3-928.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Indeed, using this file
in CCP4 fails with the message:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">"CCP4MTZfile: Mtz column
type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz
column type mismatch: SIGI-obs(+) M-Q"<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">The file contains
anomalous data. I have no problems with files
that do not contain anomalous data.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Needless to say that
Phenix uses the structure-factor file just
fine when reading it back into, say, its
validation utility.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">When I use
iotbx.reflection_file_reader, I cannot detect
any anomalies.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">I am at a loss as to how
to resolve this issue. I would like to deposit
the data as prepared by Phenix so that the PDB
tools can use them.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Anybody ran into this
issue before? Any ideas for how to resolve it?<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Many thanks in advance!<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">MM<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">_______________________________________________<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">phenixbb mailing list<br>
</blockquote>
</blockquote>
<blockquote type="cite">
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