[phenixbb] Reflection file woes phenix/ccp4/PDB

Felix Frolow mbfrolow at post.tau.ac.il
Fri Dec 16 07:03:54 PST 2011

Misha, you will be surprised how many times people were in situations similar to yours with PDB or PDB-EBI.
Myself was not able to submit data after PHENIX refinement, as I ALWAYS separate between anomalous + and - reflections
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
and PHENIX refuses to provide redundant information. 
The end is that one need to re-refine using diffraction data presentation formalism which  PDB will accept in order 
not to provide data that was not used for refinement but was chosen  for submission convenience.
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfrolow at post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Dec 16, 2011, at 16:50 , Machius, Mischa Christian wrote:

> Robbie,
> 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.
> 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. 
> Bit surprised though that no one has run into that problem before.
> Thanks for your suggestion.
> MM
> On Dec 16, 2011, at 3:54 AM, Robbie P. Joosten wrote:
>> Hi Mischa,
>> 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.
>> Cheers,
>> Robbie Joosten
>> Netherlands Cancer Institute
>> On 12/15/2011 05:40 PM, Machius, Mischa Christian wrote:
>>> Y'all,
>>> 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.
>>> The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928.
>>> Indeed, using this file in CCP4 fails with the message:
>>> "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J  CCP4MTZfile: Mtz column type mismatch: SIGI-obs(+) M-Q"
>>> The file contains anomalous data. I have no problems with files that do not contain anomalous data.
>>> Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility.
>>> When I use  iotbx.reflection_file_reader, I cannot detect any anomalies.
>>> 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.
>>> Anybody ran into this issue before? Any ideas for how to resolve it?
>>> Many thanks in advance!
>>> MM
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