Hi Martyn, I too was puzzled by the statement that "unmerged data cannot be handled properly as part of a PDB deposition."
We have deposited the unmerged original index intensities for the refinement wavelength (and for additional wavelengths used for phasing in the case of MAD) since 2005. This was based on recommendation #2 from the "Report of Task Force on Numerical Criteria in Structural Genomics" from the 2001 Airlie meeting (2nd Intl. Struct. Genomics Mtg.). http://www.nigms.nih.gov/NR/rdonlyres/14937E88-B916-4503-A29E-FA11E4B3D445/0/numerical.doc http://www.isgo.org/organization/members07/010410.html Which states that "For X-ray data, unmerged integrated intensities (omitting outliers but including systematically-absent axial reflections) should be deposited along with the final, merged intensities and amplitudes for all wavelengths and/or derivatives." We worked the RCSB staff to refine the format of the mmCIF formatted reflection containing multiple data loops for our depositions and this has been used for more than 1300 JCSG depositions and the data is retrievable from all wwPDB partner sites. Regards, Mitch -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn Symmons Sent: Tuesday, September 17, 2013 3:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] What kind of reflection data to deposit to PDB 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 > ger...@ebi.ac.uk ..................... pdbe.org > Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk > > > > > 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:ger...@xray.bmc.uu.se > ****************************************************************** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. > ****************************************************************** > Little known gastromathematical curiosity: let "z" be the > radius and "a" the thickness of a pizza. Then the volume > of that pizza is equal to pi*z*z*a ! > ******************************************************************
