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:
- Plain XYZ Coordinates called
PlainCoord. Atom types are specified by the numerical
entry in periodic table.
- XYZ Coordinates called
coord. Atom types specified by atomic name as a
character string.
- Gaussian© Cube
Files called Cube.
- Brookhaven Protein Data Bank
called pdb.
- GAMESS Coordinates via a
PERL script called PGamess.
- GAMESS Plotting Option
called Gamess Cube.
- MSI DCAR called Dcar.
- DMOL XYZ called DMOL_XYZ.
- Mopac Electrostatic Potential
called Mopac ESP.
- Mopac coordinates called
Mopac XYZ.
- MOL2 called mol2.
- MOL called mol.
- CHEM3D called Chem3d.
- 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 |