Crystallography Open Database (COD)

  • Saulius GražulisEmail author
  • Andrius Merkys
  • Antanas Vaitkus
Living reference work entry


The Crystallography Open Database (COD, is as of the time of writing the largest open-access collection of mineral, metal organic, organometallic, and small organic crystal structures, excluding biomolecules that are stored separately in the Protein Data Bank ( Unlike other existing chemical crystal structure databases, the COD is fully open – all its structures may be downloaded, used and re-disseminated without restriction, along with the results derived from them. Currently, the COD contains >385, 000 records and is growing constantly, encompassing most structures published in peer-reviewed academic press and donations by individual researchers. This article describes how data are organized in the COD and how the database can be queried, downloaded, and processed for various purposes.



This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 689868.


  1. Allen FH, Bellard S, Brice MD, Cartwright BA, Doubleday A, Higgs H, Hummelink T, Hummelink-Peters BG, Kennard O, Motherwell WDS, Rodgers JR, Watson DG (1979) The Cambridge crystallographic data centre: computer-based search, retrieval, analysis and display of information. Acta Crystallogr Sect B Struct Crystallogr Crystal Chem 35(10):2331–2339CrossRefGoogle Scholar
  2. Andronico A, Randall A, Benz RW, Baldi P (2011) Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. J Chem Inf Model 51:760–776CrossRefGoogle Scholar
  3. Aroyo MI, Perez-Mato JM, Capillas C, Kroumova E, Ivantchev S, Madariaga G, Kirov A, Wondratschek H (2006) Bilbao crystallographic server: I. Databases and crystallographic computing programs. Zeitschrift für Kristallographie – Crystalline Materials 221(1):15–27ADSCrossRefGoogle Scholar
  4. Aroyo MI, Perez-Mato JM, Orobengoa D, Tasci E, de la Flor G, Kirov A (2011) Crystallography online: Bilbao crystallographic server. Bulg Chem Commun 43(2):183–197Google Scholar
  5. Baerlocher C, McCusker LB, Olson DH (2007) Atlas of zeolite framework types, 6th revised edn. Elsevier, Amsterdam/London/New York/Oxford/Paris/Shannon/TokyoCrossRefGoogle Scholar
  6. Baldi P (2011) Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge crystallographic data centre. J Chem Inf Model 51:3029CrossRefGoogle Scholar
  7. Belsky A, Hellenbrandt M, Karen VL, Luksch P (2002) New developments in the Inorganic Crystal Structure Database (ICSD): accessibility in support of materials research and design. Acta Crystallogr B 58:364–369CrossRefGoogle Scholar
  8. Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B (1992) The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J 63:751–759CrossRefGoogle Scholar
  9. Berman HM, Kleywegt GJ, Nakamura H, Markley JL (2012) The protein data bank at 40: reflecting on the past to prepare for the future. Structure 20:391–396CrossRefGoogle Scholar
  10. Bragg WH (1913) The reflection of x-rays by crystals. (II) Proc R Soc A Math Phys Eng Sci 89(610):246–248ADSCrossRefGoogle Scholar
  11. Bragg WH, Bragg WL (1913) The reflection of x-rays by crystals. Proc R Soc Lond A Math Phys Eng Sci 88:428–438ADSCrossRefGoogle Scholar
  12. Breternitz J, Gregory D (2015) The search for hydrogen stores on a large scale; a straightforward and automated open database analysis as a first sweep for candidate materials. Crystals 5:617–633CrossRefGoogle Scholar
  13. Brown ID, McMahon B (2002) CIF: the computer language of crystallography. Acta Crystallogr B 58:317–324CrossRefGoogle Scholar
  14. Chateigner D, Grazulis S, Pérez O, Pepponi G, Lutterotti L (2015) COD, PCOD, TCOD, MPOD…open structure and property databases. accessed 2018-10-03
  15. Clews CJB, Cochran W (1948) The structures of pyrimidines and purines. I. A determination of the structures of 2-amino-4-methyl-6-chloropyrimidine and 2-amino-4,6-dichloropyrimidine by x-ray methods. Acta Crystallogr 1(1):4–11CrossRefGoogle Scholar
  16. Downs RT, Hall-Wallace M (2003) The American mineralogist crystal structure database. Am Miner 88:247–250CrossRefGoogle Scholar
  17. Faber J, Fawcett T (2002) The powder diffraction file: present and future. Acta Crystallogr B 58(3 Part 1):325–332CrossRefGoogle Scholar
  18. Fielding RT (2000) Architectural Styles and the design of network-based software architectures. Ph.D. thesis, University of California, IrvineGoogle Scholar
  19. First EL, Floudas CA (2013) Mofomics: computational pore characterization of metal-organic frameworks. Microporous Mesoporous Mater 165:32–39CrossRefGoogle Scholar
  20. Friedrich W, Knipping P, Laue M (1912) Interferenzerscheinungen bei Röntgenstrahlen. Eine quantitative Prüfung der Theorie für die Interferenz-Erscheinungen bei Röntgenstrahlen. Bayerische Akademie der Wissenschaften, Mathematisch-Physikalische Klasse, Sitzungsberichte, pp 303–322zbMATHGoogle Scholar
  21. Friedrich W, Knipping P, Laue M (1912) Interferenzerscheinungen bei Röntgenstrahlen. Eine quantitative Prüfung der Theorie für die Interferenz-Erscheinungen bei Röntgenstrahlen, II. Bayerische Akademie der Wissenschaften, Mathematisch-Physikalische Klasse, Sitzungsberichte, pp 363–373Google Scholar
  22. Gražulis S, Chateigner D, Downs RT, Yokochi AFT, Quirós M, Lutterotti L, Manakova E, Butkus J, Moeck P, Le Bail A (2009) Crystallography open database: an open-access collection of crystal structures. J Appl Crystallogr 42(4):726–729CrossRefGoogle Scholar
  23. Gražulis S, Daškevič A, Merkys A, Chateigner D, Lutterotti L, Quirós M, Serebryanaya NR, Moeck P, Downs RT, Le Bail A (2012) Crystallography open database (COD): an open-access collection of crystal structures and platform for world-wide collaboration. Nucleic Acids Res 40(D1):D420–D427CrossRefGoogle Scholar
  24. Gražulis S, Sarjeant AA, Moeck P, Stone-Sundberg J, Snyder TJ, Kaminsky W, Oliver AG, Stern CL, Dawe LN, Rychkov DA, Losev EA, Boldyreva EV, Tanski JM, Bernstein J, Rabeh WM, Kantardjieff KA (2015) Crystallographic education in the 21st century. J Appl Crystallogr 48(6):1964–1975CrossRefGoogle Scholar
  25. Groom CR, Allen FH (2014) The Cambridge structural database in retrospect and prospect. Angew Chem Int Ed 53:662–671CrossRefGoogle Scholar
  26. Groom CR, Bruno IJ, Lightfoot MP, Ward SC (2016) The Cambridge structural database. Acta Crystallogr B 72(2):171–179CrossRefGoogle Scholar
  27. Hall SR, Allen FH, Brown ID (1991) The crystallographic information file (CIF): a new standard archive file for crystallography. Acta Crystallogr A 47(6):655–685CrossRefGoogle Scholar
  28. Harrison WTA, Simpson J, Weil M (2009) Editorial. Acta Crystallogr E Struct Rep Online 66(1):e1–e2MathSciNetCrossRefGoogle Scholar
  29. Hermann C, Ewald PP (1931) Strukturbericht 1913-1928: Zeitschrift für Kristallographie, Kristallgeometrie, Kristallphysik, Kristallchemie. Akademische Verlagsgesellschaft, LeipzigGoogle Scholar
  30. IUCr (2017) A formal grammar for CIF., accessed 2018-10-03
  31. IUCr (2017) Crystallographic information framework., accessed 2018-10-03
  32. IUCr (2017) Structure reports., accessed 2018-10-03
  33. Kabekkodu SN, Faber J, Fawcett T (2002) New powder diffraction file (pdf-4) in relational database format: advantages and data-mining capabilities. Acta Crystallogr B 58:333–337CrossRefGoogle Scholar
  34. Kaduk JA (2002) Use of the inorganic crystal structure database as a problem solving tool. Acta Crystallogr B 58(Pt 3 Pt 1):370–379CrossRefGoogle Scholar
  35. Lafuente B, Downs RT, Yang H, Stone N (2015) The power of databases: the RRUFF project. In: Highlights in mineralogical crystallography. W. De Gruyter, Berlin, pp 1–30Google Scholar
  36. Le Bail A (2005) Inorganic structure prediction with grinsp. J Appl Crystallogr 38:389–395CrossRefGoogle Scholar
  37. Lejaeghere K, Van Speybroeck V, Van Oost G, Cottenier S (2014) Error estimates for solid-state density-functional theory predictions: an overview by means of the ground-state elemental crystals. Crit Rev Solid State Mater Sci 39:1–24ADSCrossRefGoogle Scholar
  38. Long F, Nicholls RA, Emsley P, Gražulis S, Merkys A, Vaitkus A, Murshudov GN (2017) ACEDRG: a stereo-chemical description generator for ligands. Acta Crystallogr D 73(2):112–122CrossRefGoogle Scholar
  39. Long F, Nicholls RA, Emsley P, Gražulis S, Merkys A, Vaitkus A, Murshudov GN (2017) Validation and extraction of stereochemical information from small molecular databases. Acta Crystallogr D 73(2):103–111CrossRefGoogle Scholar
  40. Merkys A, Vaitkus A, Butkus J, Okulič-Kazarinas M, Kairys V, Gražulis S (2016) COD::CIF::Parser: an error-correcting CIF parser for the Perl language. J Appl Crystallogr 49(1):292–301CrossRefGoogle Scholar
  41. Merkys A, Mounet N, Cepellotti A, Marzari N, Gražulis S, Pizzi G (2017) A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD. J Cheminform 9(1):56CrossRefGoogle Scholar
  42. Mounet N, Gibertini M, Schwaller P, Campi D, Merkys A, Marrazzo A, Sohier T, Castelli IE, Cepellotti A, Pizzi G, Marzari N (2018) Novel two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds. Nature Nanotechnology, 13(3):246–252ADSCrossRefGoogle Scholar
  43. Narayanan BC, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM (2014) The nucleic acid database: new features and capabilities. Nucleic Acids Res 42:D114–D122CrossRefGoogle Scholar
  44. Pepponi G, Gražulis S, Chateigner D (2012) MPOD: a material property open database linked to structural information. Nucl Instrum Methods Phys Res Sect B: Beam Interact Mater Atoms 284(0):10–14. E-MRS 2011 Spring Meeting, Symposium M: X-ray techniques for materials research-from laboratory sources to free electron lasersGoogle Scholar
  45. Perez-Mato JM, Gallego SV, Tasci ES, Elcoro L, de la Flor G, Aroyo MI (2015) Symmetry-based computational tools for magnetic crystallography. Annu Rev Mater Res 45(1):217–248ADSCrossRefGoogle Scholar
  46. Protein Data Bank (1971) Protein data bank. Nat New Biol 233:22–23Google Scholar
  47. Rajan H, Uchida H, Bryan DL, Swaminathan R, Downs RT, Hall-Wallace M (2006) Building the American mineralogist crystal structure database: a recipe for construction of a small internet database. In: Sinha AK (ed) Geoinformatics: data to knowledge, Geological Society of America, Boulder, vol 397, 73–80CrossRefGoogle Scholar
  48. Röntgen WC (1896) On a new kind of rays. Nature 53:274–276Google Scholar
  49. Sadowski P, Baldi P (2013) Small-molecule 3d structure prediction using open crystallography data. J Chem Inf Model 53:3127–3130CrossRefGoogle Scholar
  50. Sander T, Freyss J, von Korff M, Rufener C (2015) DataWarrior: an open-source program for chemistry aware data visualization and analysis. J Chem Inf Model 55(2):460–473CrossRefGoogle Scholar
  51. Villars P, Onodera N, Iwata S (1998) The linus pauling file (LPF) and its application to materials design. J Alloys Compd 279:1–7CrossRefGoogle Scholar
  52. Villars P, Cenzual K, Daams J, Chen Y, Iwata S (2004) Data-driven atomic environment prediction for binaries using the mendeleev number: part 1. Composition {AB}. J Alloys Compd 367(1–2):167–175. Proceedings of the {VIII} international conference on crystal chemistry of intermetallic compoundsGoogle Scholar
  53. White PS, Rodgers JR, Le Page Y (2002) Crystmet: a database of the structures and powder patterns of metals and intermetallics. Acta Crystallogr B 58(Pt 3 Pt 1):343–348CrossRefGoogle Scholar
  54. . . . , . 1. , . 1955Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Saulius Gražulis
    • 1
    Email author
  • Andrius Merkys
    • 1
  • Antanas Vaitkus
    • 1
  1. 1.Department of Protein-DNA InteractionsVilnius University Institute of BiotechnologyVilniusLithuania

Section editors and affiliations

  • Nicola Marzari
    • 1
  1. 1.Laboratory of theory and simulation of materialsSwiss Federal Institute of TechnologyLausanneSwitzerland

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