# STM Express Modules

# Introduction

The STM codes are a suite of application codes and AVS modules to display both geometric structure and electronic properties. Electronic and geometrical structural information is obtained from either Density Functional Theory (DFT) or Schrödinger Theory, using a variety of computational or experimental approaches. For more information see the original paper presented at the AVS97 User meeting.

# Geometric Structure

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 specified by 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.

The geometric structure reader is called `mol_c` . The User Interface for this module is in two parts:

| INPUT - The parameters that controls how the data is read. Pause the display. This pauses the module from processing and allows the user to set the input correctly (Select File Type and Units). Select the type of file to read. Select a value for the type of units. Note that for some displays the default atom-atom bond or hydrogen-atom bond values are not correct. Sliders Set Bond Scale Factor and Set Hydrogen Bond Scale Factor allow for scaling the display. Select a file to read. Uncheck the Pause. Note, when initially starting the application, you may also have to press the start button. This is due to how AVS/Express will save the application. OUTPUT Select the type of display. The display options are: Select to show or hide the hydrogen atoms. The Set Sphere Size type-in allows the user to scale the size of the atom spheres. ball and stick display spheres connected by single lines. The bonds are determined by two atoms being close (within a cutoff) specified in the module. The atoms are colored by type. cpk also known as space-filling model. The radii of the atoms are the van der Waals radii also specified in the module. colored stick is also just the bond structure colored by atom type. colored residue is a residue based display, and each residue is colored differently.

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

An example network using `mol_c` is shown below. The main connection for `mol_c` is to the `SingleWindowApp` UViewer3D module.

# Electronic Structure

The STM AVS Express modules will read data from either the Gaussian Cube Option or a plot file from GAMESS. Electron densities are obtained from Density Functional Theory (DFT) via the Kohn-Sham (KS) orbital-density equations or from wave function functional via the Schrödinger equation.

- Input of the data into AVS Express is accomplished using different input data readers which were specifically designed to read data from Gamess or Gaussian CUBE files
- Combining these modules with the reader mol_c and AVS Express built-in functions, additional molecular properties can be computed and displayed.
- Mapping these properties onto an isodensity surface, which is overlayed onto the geometric structure shows how the electronic properties relate to chemical activity.

## Gaussian Cube Reader

The Gaussian Cube Reader module reads the Gaussian Cube file output. The cube output in the example below is denoted (commonly) with a `.grd` for the density, HOMO and ESP properties, respectively.

The module is used in the following example network:

To give the following display:

## GAMESS output

The GAMESS Plot file readermodule reads the `.F33` file output from GAMESS. The file can have any extension.

The module is used in the following example network:

To give the following display: