CIF file format

The CIF file format was quickly and widely adopted by the scientific community for at least two reasons [165J it was, and still is, endorsed by the lUCr and submission of data to the journal Acta Ciystallographka, Section C in a form conforming to CI F assures faster processing and hence faster publication of accepted papers. The current CIF file dictionary defines about 1200 data names, but it is still unable to represent all the details of the crystallographic measurements of macromolecules. Thus, yet another STAR-based data format is needed. 

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The International Union of Crystallography maintains up to date information about CIF file formats and uses, as methodology continues to evolve. At present, its web address is http //www.iucr.org. 

A consideration of the whole bulk of the CSD is both impractical and unnecessary. At the same time, the Cif file format in which the CSD entries are stored requires extensive manipulation of alphabetic data and is impractical for use with computer programs written in the most widely used languages for scientific calculation. For the examples shown in this chapter, some reduced databases have therefore been prepared from the CSD, containing molecular data in numerical form. A full description of the retrieval procedure is given in the Supplementary material (see OPiX manual, Retcif-Coor procedures). 

Besides the MDL Molfile formal, other file formats are often used in chemistry SMILES has already been mentioned in Section 2.3.3. Another one, the PDB file format, is primarily used for storing 3D structure information on biological macromolecules such as proteins and polynucleotides (Tutorial, Section 2.9.7) [52, 53). GIF (Crystallographic Information File) [54, 55] is also a 3D structure information file format with more than three incompatible file versions and is used in crystallography. GIF should not be confused with the Chiron Interchange Formal, which is also extended with. cif. In spectroscopy, JCAMP is apphed as a spectroscopic exchange file format [56]. Here, two modifications can be... 

GIF. cif Crystallographic Information File format for 3D structure information on organic molecules umnv.iucr.org/iucr4op/cif/ 55... 

An alternative and much more flexible approach is represented hy the STAR file format [L48, 149, which can be used for building self-describing data files. Additionally, special dictionaries can be constructed, which specify more precisely the contents of the eorresponding data files. The two most widely used such dictionaries (and file formats) arc the CIF (Crystallographic Information File) file format [150] - the International Union of Crystallography s standard for representation of small molecules - and mmCIF [151], which is intended as a replacement for the PDB format for the representation of macromolecular structures,... 

When all the atoms of the target structure have been found and refined so that no movement/variation of any structural parameter occurs, the refinement programs will output a file which can be used for the analysis of the structure and deposition to databases, like Cambridge Crystallographic Data Centre. This file is called Crystallographic Information File, i.e. CIF file, and it has a specific and regulated format. 

The crystallographic information file (CIF) and macro-molecular CIF (mmCIF) formats developed by the International Union of Crystallography, mainly to represent the data associated with X-ray crystallography studies. 

The CIF format not only defines its dictionary of available data names, but restricts the STAR file syntax as well. For example, lines may not exceed 80 characters and data names can contain a maximum of 32 characters. Furthermore, the CIF dictionaiy specifies default units for numeric fields that represent numeric values with units. If the data item is not stored in the default units, then the units code is appended to the data name. Thus cell length a and cell length a pm represent the dimensions ofthe unit cell in Angstrom (the default units conforming to the SI Standard) and picomclcrs, respectively. 

CCDC reference number 1145/171. See http //www.rsc.org/suppdata/ jm/1999/2407 for crystallographic files in. cif format. 

Program for processing X-ray structures in the format of Crystallographic Information Files (CIF). CYCLOPS for dictionary validation. 

With CIF becoming a more used standard in the powder diffraction community, structure data conversion is becoming less needed on a day-to-day basis. The Powder Cell format is probably the next best format due to its relative simplicity compared to CIF. Most structure databases can export files into CIF format, and some to Powder Cell format. Eric Dowty s Cryscon software is currently the most comprehensive structure data conversion and transformation (Table 17.8). However, due care should be shown and results checked. Normally, the programs are robust, and it is more a case of users selecting options without understanding the consequences. 

This program [4] accepts structural data from CIF documents and from ins files. The atomic coordinates are converted into orthogonal A coordinates and a selected atom is placed at a common origin, as seen below. Other atoms are added that define a set of 3-D orientations. Least-square fitting of some, or all, atoms is performed. The choice is dictated by the extent of disagreement (or agreement) in stereochemistry of the molecules in question. To distinguish the molecules, a pair of colours is selected for the two molecular bonds, and atoms are coded by colour. Finally, the molecule is rotatable in 3-D space to locate the most convenient view the picture is labeled and saved. For the latter purpose, of several format options that are available, PAINT or WORD formats are most useful. 

The molecular information file (MIF), developed from extensions to the earlier standard molecular data (SMD) format, designed to be compatible with CIF and mmCIF and, at present at least, used primarily by the crystallographic community. 

TABLES converts actual anisotropic temperature factors to Uij and calculates equivalent isotropic thermal parameters fieq and t/eq from TABLES also calculates the following items by a keyword (i) bond distances, angles, and torsion angles are tabled with their standard deviation in parentheses (ii) molecular weight Mr, calculated density D, and absorption coefficient /x (iii) a list of reflection data. The necessary data to submit to lUCr are written on a file automatically in CIF format. 

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