Conversion from CIF to PDB or XYZ

The ImportCIF conversion algorithm in FFX relies on two input files. The first being the CIF we wish to convert. The second is a PDB or XYZ file that will supply parameters for the converted structure (Note: The ImportCIF converter does not generate parameters. Parameterization needs to occur prior to conversion. For more information on creating input files, see here). Finally, the CIF and PDB/XYZ files should have different names because ImportCIF will create a PDB or XYZ file (depending on the input file format) with the same name as the provided CIF. The command may look something like:

                    ffxc ImportCIF NAME.cif NAME.pdb
                    or
                    ffxc ImportCIF NAME.cif NAME.xyz
                

There should be a newly generated PDB/XYZ and Properties file with the same name as the selected CIF file (in the above examples: NAME.pdb and NAME.properties or NAME.xyz and NAME.properties, respectively). The files should be ready for further calculations, but it is recommended that Minimize and/or MinimizeCrystals is performed as newly converted files tend to be in strained conformations with respect to the applied model.

ImportCIF can handle appended CIFs, however, in the case of XYZ format, the space group of the CIF will be appended to the file name as appended CIFs may have different space groups, but appended XYZ (aka ARC) files must consist of a single space group specified in the Properties file (e.g. NAME_P21c.arc and NAME_P21c.properties). ImportCIF can attempt to fix crystal parameters to conform to the supplied lattice system, but since this alters the structure from the original CIF, the user must indicate that this is desired by adding the "--fixLattice" or "--fl" flag to the command. The default values are sufficient for most cases, but additional options can be seen through the help message:

ffxc ImportCIF --help
                

From PDB or XYZ to CIF

The ImportCIF conversion algorithm also allows for the conversion to CIF format. However, this will require a PDB or XYZ file that has been parameterized. (Note: The ImportCIF converter does not generate parameters. Parameterization needs to occur prior to conversion. For more information on creating input files, see here). Finally, the "--saveCIF" or "--sc" flag should be added to the command. The command may look something like:

ffxc ImportCIF --sc NAME.xyz
                

The result from the above command should be a generally formatted CIF with the coordinates and crystallographic information of the original XYZ.

Utilized Software

The ImportCIF converter uses CIFTools provided by the RCSB (CIFTools¹) and objects provided by the Chemistry Development Kit (CDK²)

Conversion from XYZ to PDB

The SaveAsPDB conversion algorithm only needs the parameterized XYZ file as input. (Note: Again, parameterization needs to occur prior to conversion. For more on creating input files, see here).

ffxc SaveAsPDB NAME.xyz
                    

ffxc Biotype NAME.xyz
                    

biotype    1  O1  "NAME         "  415 C11
                    

Conversion from PDB to XYZ

If you are utilizing parameters outside the default force field, you will need to have access to Biotype records to map the parameters to the corresponding atoms. Assuming all atoms in the system are defined (either by the force field or seperate parameter file) the following command should be sufficient to convert a PDB file to an XYZ:

ffxc SaveAsXYZ NAME.xyz