Sorry to contradict,
But the mmCIF data model certainly does not seem to require hkl unique
within the reflection data.
Like CIF the mmCIF formalism has been developed to allow a complete
description of a diffraction experiment and the data arising from it.
There is a full description at
http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html
(I am grateful to Rachel Kramer Green at the RCSB for pointing out these
links to the dictionary and the papers describing its development).
Having chosen mmCIF for the archive and then not using its flexibility
seems a bit like having your cake and NOT eating it.
It is strange to hear on a discussion board that recently considered the
advantages of depositing complete image data, that a case will have to
be made for allowing the deposition of full unmerged datasets.
++Martyn
On 16/09/2013 14:03, Gerard DVD Kleywegt wrote:
Dear all,
At present, unmerged data cannot be handled properly as part of a PDB
deposition. One reason for this is that changes to the mmCIF/PDBx data
model will be required (at the moment, hkl must be unique within the
reflection data, which is logical for merged data but precludes
handling of unmerged data). There are other (easier to resolve) issues
to work out, e.g. having to do with file naming and distribution via
the wwPDB ftp archive.
The wwPDB partners are presently focusing all efforts on rolling out
the new joint deposition and annotation system. Once this system is
reasonably stable we will look into accepting/validating/distributing
new kinds of data. This concerns not only unmerged Is for X-ray but
also unassigned NOE peak lists for NMR. We will seek the advice of the
corresponding wwPDB VTFs (Validation Task Forces) to help define the
data items that need to be captured, how the data should be processed
by wwPDB, and what kind(s) of validation is/are required.
--Gerard
---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
[email protected] ..................... pdbe.org
Secretary: Pauline Haslam [email protected]
On Thu, 5 Sep 2013, Raji Edayathumangalam wrote:
Hi Folks,
Sorry for the non-ccp4 post.
I am trying to determine what is the best form of unmerged reflection
data
to deposit to the PDB. I have single wavelength anomalous data for my
structure and I have two flavors of scaled files from the same exact
set of
diffraction images: (1) data indexed and scaled in p1, and (2) data
indexed
in p222, scaled in Scalepack using the "no merge original index"
option and
converted to .mtz since the unit cell in the header of the output
.sca file
was missing.
The space group for the dataset is p212121.
Please could you let me know what might be the best approach.
Many thanks and cheers,
Raji
--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:[email protected]
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