Re: [phenixbb] observed reflections error?

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 To: [email protected] Sent: Wednesday, 26 February 2014, 9:25 Subject: Re: [phenixbb] observed reflections error? -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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:[email protected]] Sent: Tuesday, 25 February 2014 10:21 a.m. To: Joel Tyndall Cc: [email protected] 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 mailto:[email protected]> 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 7293tel:%2B64%203%20479%207293

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