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 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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

_______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

- -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTDbL9UxlJ7aRr7hoRAqPTAKCfRArE1RzIG8O7WFIthz4waUcHRgCeLc04 D/JwT7gkuiZ6shtJ03dVBcw= =/ReF -----END PGP SIGNATURE----- _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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   Martyn     ________________________________ From: Tim Gruene To: MARTYN SYMMONS Cc: "[email protected]" 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. Best, Tim 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 To: [email protected] 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:[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

...

_______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

...

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A