- Ligplot - You don't need any skills to use Ligplot. Only thing you have to give is the "residue number" of the ligand or the small molecule you are interested in the command line.
- leview - is a ligand environment viewer that plots environments of ligands in various view types. At the moment is only works on existing structures since the ligands have to be correctly typed with correct dictionaries. This has a number of export formats.
- EBIAstexViewer - also has a chemistry viewer (menu -> Chemistry) which shows the ligand in 2D with the environment and various options.