# Welcome to the STM
Running STM

UNIX | Windows
The Run script will run the STM application. | The Run.bat batch file will run the STM application. On a windows system, you can create and edit a desktop icon (see the FAQ page.)

The STM application User interface controls both the input parameters (describing the characteristics of the input file) and display parameters (describing the images viewed). For more information read this page.

| 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 File Type Select the type of file to read. Units 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.

The STM application comes with several pre-constructed networks (the networks are in the v directory) to display data from a variety of file formats and display options. The networks are described below:

- MolecularDisplayApp.v - this network will read and display molecular structure. Each file format has an associated test data file:

  Data Files for the molecular data test.
  File Name | File Size | Select File Type
  PlainCoord.dat | 840 | Plain XYZ Coordinates called Set PlainCoord. Atom types specified by the numerical entry in periodic table.
  COORD.dat | 2,101 | XYZ Coordinates called Set coord. Atom types specified by atomic name as a character string.
  CUBEpot.dat | 542 | Gaussian© Cube Files called Cube.
  tryp_den.grd | 1,690,138 | Gaussian© Cube Files called Set Cube.
  tryp_homo.grd | 1,690,155 | Gaussian© Cube Files called Set Cube.
  tryp_pot.grd | 1,690,223 | Gaussian© Cube Files called Set Cube.
  PDB.dat | 869 | Brookhaven Protein Data Bank called Set pdb.
  caffine.pdb | 2,495 | Brookhaven Protein Data Bank called Set pdb.
  PGamess.dat | 235 | GAMESS Coordinates via a PERL script called Set PGamess.
  exam01.new | 3,309,142 | GAMESS Plotting Option called Set Gamess Cube.
  jerry.F33 | 6,168,938 | GAMESS Plotting Option called Set Gamess Cube.
  DCAR.dat | 1,081 | MSI DCAR called Set Dcar.
  DMOLxyz.dat | 1,078 | DMOL XYZ called Set DMOL_XYZ.
  MOPACesp.dat | 570 | Mopac Electrostatic Potential called Set Mopac ESP.
  MOPACxyz.dat | 380 | Mopac coordinates called Set Mopac XYZ.
  Mol2.dat | 2,412 | MOL2 called Set mol2.
  Mol.dat | 457 | MOL called Set mol.
  Chem3d.dat | 323 | CHEM3D called Set Chem3d.
  MM3.dat | 619 | Molecular Mechanics Code MM3 called Set mm3.

- animatedMolDisplay.v - this network is designed to read a sequence of files and display the data. To test this network, use the files below:

  Data Files for the animated test. These are all Plain Coordinate files.
  File Name | Size
  DWB.0001 | 840
  DWB.0002 | 840
  DWB.0003 | 840
  DWB.0004 | 840
  DWB.0005 | 840
  DWB.0006 | 840
  DWB.0007 | 840
  DWB.0008 | 840
  DWB.0009 | 840
  DWB.0010 | 840
  DWB.0011 | 840
  DWB.0012 | 840
  DWB.0013 | 840
  DWB.0014 | 840
  DWB.0015 | 840
  DWB.0016 | 840
  DWB.0017 | 840
  DWB.0018 | 840
  DWB.0019 | 840
  DWB.0020 | 840
  DWB.0021 | 840
  DWB.0022 | 840
  DWB.0023 | 840
  DWB.0024 | 840
  DWB.0025 | 840
  DWB.0026 | 840
  DWB.0027 | 840
  DWB.0028 | 840

- G94CubeDisplay.v - this network is designed to read the output generated by the CUBE option from Gaussian. The Set File Type option is Set Cube. To test this network, use the files below:

  Data Files for the molecular data test.
  File Name | Size | File Type
  CUBEpot.dat | 542 | Gaussian© Cube Files called Cube.
  tryp_den.grd | 1,690,138 | Gaussian© Cube Files called Cube.
  tryp_homo.grd | 1,690,155 | Gaussian© Cube Files called Cube.
  tryp_pot.grd | 1,690,223 | Gaussian© Cube Files called Cube.

- GamessCubeDisplay.v - this network is designed to read a file output from GAMESS (the log file processed by a PERL script) and display the data. To test this network, use the files below:

  Data Files for the molecular data test.
  File Name | Size | File Type
  exam01.new | 3,309,142 | GAMESS Plotting Option called Gamess Cube.
  jerry.F33 | 6,168,938 | GAMESS Plotting Option called Gamess Cube.