# STM: Molecular Geometry

Geometric structures are read from data files which contain either experimental or computed structure information. The STM codes can read structural information from:

1. Plain XYZ Coordinates called PlainCoord. Atom types are specified by the numerical entry in periodic table.
2. XYZ Coordinates called coord. Atom types specified by atomic name as a character string.
3. Gaussian© Cube Files called Cube.
4. Brookhaven Protein Data Bank called pdb.
5. GAMESS Coordinates via a PERL script called PGamess.
6. GAMESS Plotting Option called Gamess Cube.
7. MSI DCAR called Dcar.
8. DMOL XYZ called DMOL_XYZ.
9. Mopac Electrostatic Potential called Mopac ESP.
10. Mopac coordinates called Mopac XYZ.
11. MOL2 called mol2.
12. MOL called mol.
13. CHEM3D called Chem3d.
14. Molecular Mechanics Code MM3 called mm3.

A partial list of the atom type colors.

Atom Type | Color
Hydrogen | White
Carbon | Green
Oxygen | Red
Sulfur | Yellow
Nitrogen | Blue
Heavy Atoms | Gray or purple