Prequest: 4.1 CIF

Back to File Formats


This format has been in existence since 1976, with some variations. The PreQuest program will cope with most files from different versions of SHELX. You may provide the SHELX instruction file if that is all that is available (filename.ins) but it is much better to provide the output file which contains the co-ordinate e.s.d's, and the list of bond lengths with e.s.d. (filename.res).

Since the SHELX format does not include the space group symbol PreQuest uses the LATT and SYMM fields to construct the pattern of operators stored in CSD, and looks up a definitive table of space group symbol versus symmetry operators to provide the text symbol e.g. Pbca.

No special handling of disordered atoms is carried out, these will require attention using the 3D Edit function.

4.3 MOL

PreQuest accepts MOL files: the input file for the MDL MACCS system. MOL files (Dalby et al., J. Chem. Inf. Comput. Sci., 1992, 32, 244-255) are widely used for storage of Cartesian co-ordinate data, e.g. from NMR studies.

PreQuest extracts the atom and bond blocks, preserving the MDL bond types (single, double, and triple bonds only). Any leading information in lines 1 to 3 of a MOL file will be treated as the Compound title.

Note: In order for the CSD and Quest to operate uniformly over Cartesian and fractional crystallographic co-ordinates we use a convention whereby the co-ordinate data are placed in a cubic unit cell of axes 100Å, the space group is set as P1, and the co-ordinates are stored as x/100, y/100, z/100.

All intramolecular 3D searches work on the Cartesian co-ordinate entries in the same way as they do for ordinary main file crystallographic entries.

4.4 MOL2 Format

This format is used by the Tripos Sybyl program and many molecular modelling "structures" are stored using it. PreQuest extracts as much information as can be stored in the CSD format and the first line following <TRIPOS> MOLECULE is copied to #COMPND as the compound name.

Note that Tripos atom types cannot be stored in CSD, only the element symbol. The <TRIPOS> BOND fields are stored with bond types as given.

Back to File Formats

PreQuest: 4.5 BCCAB Format .