<html><head></head><body 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; color: rgb(0, 0, 0); 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; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -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 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>
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<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"><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote></blockquote><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br></div></body></html>