One way of deriving a dictionary entry is using a PDB-style connectivity list as shown in Text 1. Extreme care should be taken when using a PDB-style connectivity list as it is a formatted file and all atoms including hydrogens must be present with all their connectivity. If at least one atom (for example hydrogen) is absent, the whole geometry of the ligand may become incorrect as the program will interpret bonds incorrectly. When the connectivity list is ready, LIBCHECK can be used to derive a minimum description:
libcheck << eol _file_dic my_pdb_connectivity.dic eol
The program LIBCHECK will create a minimum description as in Text 2 and it will be written to new_mon_lib.cif. Then this file should be copied to another file and checked carefully. After checking, an editing technique described in the section "dictionary entry from minimum description" should be used to derive a dictionary entry and coordinates to be used by the graphics program.
After editing the minimum description to the user's satisfaction, it can be used to derive a new entry list and coordinates using LIBCHECK.