Crystallography Open Database

Abstract: Using an open-access distribution model, the Crystallography Open Database (COD, http://www .crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated � 150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

Abstract: A database has been constructed that contains all the crystal structures previously published in the American Mineralogist. The database is called “The American Mineralogist Crystal Structure Database” and is freely accessible from the websites of the Mineralogical Society of America at http://www.minsocam.org/MSA/Crystal_Database.html and the University of Arizona. In addition to the database, a suite of interactive software is provided that can be used to view and manipulate the crystal structures and compute different properties of a crystal such as geometry, diffraction patterns, and procrystal electron densities. The database is set up so that the data can be easily incorporated into other software packages. Included at the website is an evolving set of guides to instruct the user and help with classroom education. parameters; (5) incorporating comments from either the original authors or ourselves when changes are made to the originally published data. Each record in the database consists of a bibliographic reference, cell parameters, symmetry, atomic positions, displacement parameters, and site occupancies. An example of a data set is provided in Figure 1. The first part of each data set contains identifying information, bibliography and notes, while the second part contains the crystallographic parameters. The first line of a data file contains an identifier, such as the name of the mineral or formula of the chemical species. The next line(s) contain the names of the authors, each separated by a comma. This is followed by the journal reference, title of the paper, and additional notes. The crystallographic data begins with a listing of the cell parameters and space group. If the data is given with respect to a non-standard space group origin then an asterisk precedes the space group symbol and the next line contains the translation vector from the standard origin. The 1952 edition of the International Tables for X-ray Crystallography are used to define the standard origin. The rest of the data set is a fixed-formatted listing of the atoms, their positional and displacement parameters, and occupancies. A header is provided that defines rightjustified columns. The name of each atom identifies the occupying elements, with additional identifiers added when appropriate. For instance, “Oco” identifies a particular oxygen atom in the albite structure. Some data sets report a crystallographic site occupied by molecular species rather than elemental, such as OH, water or methane. In most of these cases the atom name is denoted by molecular formula. For example, “CH4” denotes methane, and “Wat” denotes water. The displacement factors are tabulated in one of two formats, U’s or b’s

Abstract: QUALX2.0 is the new version of QUALX, a computer program for qualitative phase analysis by powder diffraction data. The previous version of QUALX was able to carry out phase identification by querying the PDF-2 commercial database. The main novelty of QUALX2.0 is the possibility of querying also a freely available database, POW_COD. POW_COD has been built up by starting from the structure information contained in the Crystallography Open Database (COD). The latter is a growing collection of diffraction data, freely downloadable from the web, corresponding to inorganic, metal–organic, organic and mineral structures. QUALX2.0 retains the main capabilities of the previous version: (a) automatically estimating and subtracting the background; (b) locating the experimental diffraction peaks; (c) searching the database for single-phase pattern(s) best matching to the experimental powder diffraction data; (d) taking into account suitable restraints in the search; (e) performing a semi-quantitative analysis; (f) enabling the change of default choices and strategies via a user-friendly graphic interface. The advances of QUALX2.0 with respect to QUALX include (i) a wider variety of types of importable ASCII file containing the experimental diffraction pattern and (ii) new search–match options. The program, written in Fortran and C++, runs on PCs under the Windows operating system. The POW_COD database is exported in SQLite3 format.

Abstract: Data curation practices of the Crystallography Open Database (COD) are described with additional focus being placed on the formal validation using the Crystallographic Information Framework (CIF). The cif_validate program, capable of validating CIF files against both the DDL1 and the DDLm dictionaries, is presented and used to process the entirety of the COD. Validation results collected from over 450 000 CIF files are demonstrated to be a useful resource in the data maintenance process as well as the development of the underlying ontologies. A set of programs intended to aid in the dictionary migration from DDL1 to DDLm is also presented.