This is the list of STM3 modules in the October 10th, 2003 version.
The standard AVS/Express documentation instead provides reference for the standard modules used or modified inside STM3.
The modules are grouped by function:
| Readers | Readers for various, static and dynamic, chemical file formats. |
| Molecular Modules | Modules that compute various derived structures from the molecule. |
| Utility Modules | Manipulation of molecules like atom selection. |
| Crystallography Modules | Unit cells, periodic lattices and symmetries support. |
| Gaussian Cube Utility Modules | Gaussian output density cubes visualization and manipulation. |
| Display | Final rendering of molecular data, legends and interaction with the viewer. |
| Output | Output to image files, movies and other formats of the visualized information. |
| Full Applications | Ready to run applications. |
| Hidden Modules | Modules used, but not directly accessible from the STM3 library. |
To start using STM3 drag one of the Full Applications modules (MolDisplayApp or AnimDisplayApp for example) to the Network Editor area.
| Read Molecule | Read various chemistry data formats |
| Read Anim Molecule | Read animated chemistry data formats |
| Read Gaussian Cube | Read Gaussian cube density data |
| Compute SE Surface | Compute the molecule Solvent Excluded Surface using the MSMS (Molecular Surface Computation Home Page - Michel F. Sanner) tool. |
| Accumulate Traces | Accumulate traces (accumulated positions) for specific atoms in a sequence of time steps |
| NCAC Tube | Compute the N-CA-C tube |
| Find Tetrahedra | Display tetrahedra around specific atoms |
| Particle Density | Compute the average particle mass density using uniform binning |
| Velocity Mean | Compute the average particle velocity using uniform binning |
| Select Atoms | Select specific atoms (pass, remove, pass similar, remove similar) |
| Select Residues | Select residues (pass, remove, pass similar, remove similar) |
| Add Bonds | Manually add bonds between atoms |
| Cut Surface | Cut a surface (eg. the Solvent Excluded Surface) with a plane |
| Bicolor Surface | Color a surface on one side only |
| Count Bonds | Add as atom parameter (the atom charge field is used) its number of bonds |
| Crop Atoms | Crop the molecule inside a box, cylinder or sphere |
| Threshold Charge | Select atoms whose charge value meets various criteria |
| Display Unit Cell | Display the boundary of the crystal unit cell |
| Replicate Lattice | Replicate the molecule unit cell to form the crystal lattice |
| Miller Plane | Visualize the plane identified by given Miller indices. Optionally remove atoms above or below it |
| Recompute Bonds | Recompute bonds after a molecule replication |
| Crop Unit Cell | Extract a subcell from the unit cell with sides parallel to those of the unit cell itself |
| Apply Symmetries | The input molecule atoms are duplicated according to its space group symbol symmetries |
| Isosurface | Create an isosurface for a given density cube |
| Cube on Surface | Map density values on a given surface |
| Float 2 Byte | Transform a cube with float values to byte values suitable for volume rendering |
| Display Molecule | Display the molecule with selectable quality and performance levels |
| Color Legend | Display a legend for the molecule representation colors (charge values or atom type color codes) |
| Pick Atom | Display information on the picked atom (pick using ctrl-click) or distances and angles |
| output image | Make a hardcopy of the screen |
| make movie | Create a movie |
| Write POV Ray | Write the current view as a POV-Ray raytracer scene |
| Write PDB | Output the molecular structure in PDB format (with animation support) |
| MolDisplayApp | Read and display a molecule |
| AnimDisplayApp | Read and display a molecule animation |
| PickMoleculeApp | Same as MolDisplayApp plus the atom picking feature |
| TracesDisplayApp | Display traces (accumulated positions) for specific atoms in a molecule traiectory |
| Scat2VolumeApp | Display atoms as transparent/not transparent spheres depending on the charge value |
| ParticleDensityApp | Display particle mass density as an isovolume |
| MolViewer | The modified viewer used by the various full applications |
| MolecularDataType | Datatype used by the modules that operate on molecular data |
| DisplayParams | Datatype that carries information on how the molecules are renderend on screen |
| Scat to Volume | Convert the molecule to an uniform volume in which sites occupied by atoms are are represented as spheres of points. Each point has value corresponding to the charge atom value. |