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  • January 2014

Blog January 2014

  1. CIFs & Structure Factors: Improvements to Deposition & Request

    Peter Wood – Thu, 23 Jan 2014 10:29:00 GMT

    ​Experimental structure factor information is extremely important to the crystallographic community, both for the effective validation of crystal structures as well as the opportunity to revisit a refined model and attempt to extract more details from the data. The IUCr have led the way in this regard, with structure factor data requested and made available for their own journals since the mid-1990s. Since 2011, the IUCr has also recommended that publishers require authors to provide structure factors alongside any reported crystal structures to enable checking and archiving the data. At the same time the CCDC announced that structure factors would be accepted alongside Crystallographic Information Files (CIFs) for deposition to the Cambridge Structural Database (CSD).

    It is now quite common for CIFs to include structure factor information embedded within them (rather than as separate HKL or FCF files) as well as some refinement details (e.g. the contents of RES files). This means that CIFs may be considerably larger in terms of file size compared to files without this extra embedded data. As part of our on-going efforts to make data deposition smoother and easier for contributors, we have now made it possible to upload a zipped folder of CIF, HKL and/or FCF files with a total size of up to 10MB. The CCDC Deposit a Structure webpage encourages both depositions relating to scientific publications as well as private communications of structures that are not intended for publication elsewhere.

    Continue reading…

  2. Make Private Communications your New Year’s resolution!

    Seth Wiggin – Tue, 14 Jan 2014 13:44:00 GMT

    ​Crystallography is unique amongst scientific disciplines in that so many data are published and available for others to investigate and utilise.  Databases containing records and data from crystallographic experiments (including the CSD, ICSD and PDB) were founded early when the number of experiments being carried out was small. This undoubtedly helped the culture of the community (most crystallographers take it for granted that such databases exist and provide useful data) and has provided comprehensive collections of crystal data. If such databases did not exist and had to be started now, the task would appear overwhelming; the task of keeping the CSD up to date with the number of crystal structures currently published is by no means trivial!

    However, every crystallographer has structures that for one reason or another don’t get published, and many scientists have structures in a PhD thesis that they never quite got round to writing up.  After all the time, effort (and money) it takes to synthesise a compound, collect crystal data and complete refinement, many structures end up languishing on a hard drive or in a PhD thesis on a shelf.   You may not consider your crystal structure(s) to be significant to your research, but aspects of the structure determination experiment or the structure itself (e.g. bonds, angles, torsions, ring geometries), whether conventional or novel, may be significant to another researcher. Adding the structure to the CSD will help others identify the compound (using our free CellCheckCSD software), and add to the body of knowledge about molecular geometry and crystal packing.

    Continue reading…

  3. What’s new in data deposition?

    Jenny Field – Fri, 03 Jan 2014 15:02:00 GMT
    ​We are always looking for ways to get data into the Cambridge Structural Database (CSD) more quickly and efficiently, so we are delighted to have new data deposition arrangements with the International Union of Crystallography (IUCr). They have started depositing small molecule X-ray crystal data for all their journals with us prior to a journal’s publication. We then issue CCDC deposition numbers, and for the first time CCDC numbers will be published in IUCr journals (referred to as CCDC references).

    Continue reading…

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