Re: [phenixbb] observed reflections error?

28 Feb 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
  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