This website provides a means to convert chemical X-ray structures that are in Crystallographic Information File (or CIF) format to Protein Data Bank (PDB) format, which is sometimes more suitable for macromolecular applications. CIF's can be obtained freely from the Crystallography Open Database (COD).

The program does not use any of the CIF libraries which are available and makes a number of assumptions when reading the files, so it cannot be guaranteed to work every time, sorry! It should work if the coordinate data are preceded by "_atom_site_label" or "_atom_site_type_symbol" lines and end with a "loop_" line. Anisotropic U-values and partial occupancies are not handled at all, but isotropic U-values are converted to B-factors in the PDB file. Since PDB format restricts the atom name to 4 characters, some atom names are simplified. The default option is to exclude hydrogen atoms, although this only works if the "_atom_site_type_symbol" field is present in the CIF. Symmetry info is written to the PDB file so that the crystal lattice can be drawn with Coot, although Coot can generally read CIF's perfectly well without conversion to PDB first! Some CIF's do not contain any atomic coordinates and, in these cases, all that can be written to the PDB file is the cell and symmetry!

The fractional coordinates in the CIF's are orthogonalised using the PDB convention and this process is described here. These calculations are now done in the client browser so no files are uploaded to the server.

This website was put together by jbcooper_at_fastmail_dot_net and use of it comes with no warrantees, etc. The script (which can be downloaded within the html of the main page) is written in Lua and uses Fengari to communicate with Math.js. All the web site files can be obtained here: here.

Corrections and suggestions for improvements are gratefully received and please let me know if you find any CIF's which don't work. The site should now be more reliable than it was before with large CIF's or larger numbers of CIF's. It would be useful to hear if that is the case.