[phenixbb] observed reflections error?

MARTYN SYMMONS martainn_oshiomains at btinternet.com
Fri Feb 28 03:55:33 PST 2014

Dear Tim 
   that's a great point and I hope the PDB are working towards that now they have finally got a more flexible Deposition and Annotation system working. I guess one stumbling block is authors worried that people will second guess their space group assignment - but what you suggest is a good compromise on the road to full deposition of raw data. 
 All the best

 From: Tim Gruene <tg at shelx.uni-ac.gwdg.de>
To: MARTYN SYMMONS <martainn_oshiomains at btinternet.com> 
Cc: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org> 
Sent: Friday, 28 February 2014, 8:50
Subject: Re: [phenixbb] observed reflections error?

Dear Martyn,

the PDB should allow (better: enforce) the deposition of unmerged data.
This would overcome these problems because everyone can then check with
the program of their choice.


On 02/28/2014 02:26 AM, MARTYN SYMMONS wrote:
> Dear Tim-
> this can be a problem because PDB rule is that the unique non- anomalous is used for reflection count* And if the data collection remark (Remark 200) follows that and quotes for unique; while the refinement (Remark 3) quotes total used (anomalous) it can be difficult to check what fraction of the 'Unique' data was used (I know you will say 'all of the data' but it is nice to see the numbers match... just as a check). May have been sorted with mmCif categories - don't know about new deposition system with that format.
> all the best
> Martyn
> Cambridge
> *http://www.wwpdb.org/documentation/format32/remarks1.html#REMARKs 200-265
> ________________________________
>  From: Tim Gruene <tg at shelx.uni-ac.gwdg.de>
> To: phenixbb at phenix-online.org 
> Sent: Wednesday, 26 February 2014, 9:25
> Subject: Re: [phenixbb] observed reflections error?
> Dear J,
> if I understood George Sheldrick correctly, scaling under the
> assumption that Friedel's Law holds is actually the method of choice:
> the doubled multiplicity is important for stable scaling and
> apparently does not hamper with the Bijvoet differences.
> I assume this is why it is the default in most scaling programs to not
> take anomalous differences into account.
> Is there a reason why you worry about the different counting, now that
> you now the reason?
> Best,
> Tim
> On 02/25/2014 09:48 PM, Joel Tyndall wrote:
>> Hi all,
>> Indeed this is the source of the discrepancy as we scaled our data
>> without separating anomalous data. I am in the process of
>> "reprocessing" with this data but another workaround is to not use
>> the anomalous data under Data - options> advanced - no anomalous.
>> (Thanks Boaz)
>> Cheers
>> J
>> From: Nathaniel Echols [mailto:nechols at lbl.gov] Sent: Tuesday, 25
>> February 2014 10:21 a.m. To: Joel Tyndall Cc:
>> phenixbb at phenix-online.org Subject: Re: [phenixbb] observed
>> reflections error?
>> Unlike most other programs, phenix.refine counts F+ and F- as
>> separate reflections if both are present in the MTZ file - could
>> this be the source of the discrepancy?
>> -Nat
>> On Mon, Feb 24, 2014 at 1:17 PM, Joel Tyndall
>> <joel.tyndall at otago.ac.nz<mailto:joel.tyndall at otago.ac.nz>> wrote: 
>> Hi all,
>> I have a minor issue with phenix reporting the number of observed
>> reflections in the output pdb file where it appears to be roughly
>> double (120080 ) to what is actually in an mtz file (~65000) from
>> scala.
>> Any suggestions where this number might originate from?
>> Joel
>> _________________________________ Joel Tyndall, PhD
>> Associate Professor in Medicinal Chemistry National School of
>> Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand 
>> Skype: jtyndall
>> Ph: +64 3 479 7293<tel:%2B64%203%20479%207293>
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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