Converting CIF to STR files

The CIF file format (Crystallographic Information File) is a standard file format specifically developed for the exchange of crystal structure data. CIF files can be downloaded from various resources, such as the Crystallography Open Database and the American Mineralogist Crystal Structure Database. For this tutorial, download and extract the example files: Cif-Files.zip.

CIF files cannot be used by BGMN directly. They must be converted to BGMN’s proprietary structure file format (*.str). This can be done by Profex‘ structure file import. If the imported CIF files contain all information required by BGMN, the import feature works fully automatic. However, CIF files often lack some important information or use ambiguous Hermann-Mauguin symbols. In that case, import in Profex requires some user interaction. The following examples demonstrate how to import CIF files with and without user input.

Start Profex, and select „File → Import Structure File…“.

Select the file „Vaterite.cif“ from the examples offered for download above. It will be opened in the following dialog:

There are no warnings printed at the bottom of the dialog, and no dialogs prompted for user input. This is the ideal case with complete CIF files. All we have to do is to check that the PHASE name and GOAL only contain letters and digits, but not any of the following characters: <space> _ / \ + – *. The following names would be illegal: „Ca Carbonate“, „Ca-Carbonate“, „Ca_Carbonate“. The following names are allowed: „CaCarbonate“, „CaCO3“, „Vaterite“. If illegal characters are present by default, replace them. Then click „Save STR“ to save the file in the Structure database directory. It will immediately become available in Profex.

Structure file directories are usually found in the following locations:

Windows: ...\Profex-BGMN-Bundle\Profex\Structures
Mac OS X: .../Profex-Bgmn-Bundle/Structures
Linux: unspecific

For Linux (optionally also for Windows and OS X), check „Edit → Preferences → BGMN → Structure Files Directory“.

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Nicola Döbelin, July 2023