Welcome to the STM

Running STM

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.