[phenixbb] Reflection file woes phenix/ccp4/PDB - Resolved

Tue Dec 20 12:37:40 PST 2011

Hi,

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!

All the best,
Pavel

On 12/20/11 12:26 PM, Machius, Mischa Christian wrote:
> Y'all,
>
> Thanks for your comments, suggestions and empathy.
>
> 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.
>
> Cheers!
>
>
>
> On Dec 16, 2011, at 10:03 AM, Felix Frolow wrote:
>
>> 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 <mailto: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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>>>
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