Although Mol2Mol is not a modeling program, it has a simple graphical interface, but no facilities such as screen dumps and plotting are included (nearly all of the supported source or target programs can do it well!) It can display the file on the screen in different graphical formats (ball-and-stick, vector and stereo displays).

Structures may be corrected to change atom or bond types, to add or remove hydrogens etc. For advanced users the manual editing of the ASCII files is also possible. It possesses chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added.

Facilities are also provided to calculate geometrical data, such as basic distances, angles, dihedral angles around an atom, piramidality, distances from least square planes or methyl centroids, planarity and puckering of rings, checking for mistakes in protein backbones, renumbering, POV-ray... and much more!

More about Mol2Mol at its homepage: http://www.gunda.hu/mol2mol