All of these programs are installed with a standard library of CIF files.
There are several options for obtaining a CIF file for a non-standard ligand:
- go to en.wikipedia.org and enter your ligand's name, e.g. Dibenzothiophene
- copy the SMILES string provided for many small molecules in Wikipedia (of course there are many other sites where you could find SMILES strings!)
- go to http://http://grade.globalphasing.org and paste the SMILES string
- download the CIF-file
JLigand is a graphical CCP4 program. Just start a new ligand, define and link the atoms that make up your ligand, together with the hydrogens. Then regularise and save the restraint file.