STM4 module list

This is the list of STM4 modules in the 20110421 version.

The standard AVS/Express documentation provides instead reference for the standard modules used or modified inside STM4.

The modules are grouped by function:

Readers WritersReaders and writer for various, static and dynamic, chemical file formats plus movies and images production.
BondsBonds computation, editing and management.
ModulesModules that compute derived structures.
SelectionSelector modules to extract a subset of the atoms.
TrajectoriesModules related to dynamic data.
CrystallographyUnit cells, periodic lattices and symmetries support.
VolumeRendering of volumetric data like Gaussian cubes.
DisplayRendering of chemical structures and other graphical objects.
Probe and MeasureInteract with the structures: measure and editing.
Full AppsReady to run applications (plus display of the STM4 version).
ExperimentalModules not intended for general usage.
  • Crystal Fingerprints
Modules for analyzing USPEX output.
  • Align Structures
Modules to align structures given two sets of corresponding atoms.
DataypesDefinition of data types used by the STM4 library.

To start using STM4 drag one of the Full Applications modules (MolDisplayApp for example) to the Network Editor area.

Readers Writers

Read StructureRead structural and volumetric chemical data.
Read Structure No BondsRead a structure from file without computing bonds.
Read ScalarRead a set of scalar values from a file.
Read VectorRead a set of 3D vector values from a file.
Make MovieCapture a sequence of frames, one for each different viewer content, and assemble them in a movie (AVI or MPEG).
Output ImageSave a snapshot of the content of the current viewer.
Write StructureWrite a single structure or a trajectory to a chemistry data file in the selected format.
Write POV RayWrite the current view as a POV-Ray raytracer scene.
Read Fermi SurfaceRead a file in EIGENVAL format and output a volume that, using Isosurface or Isosurface nest, display the Fermi surfaces at a given energy level.
Read Fermi BandsRead a file in EIGENVAL format and output for all bands their energy along a given polyline.
Write SummaryWrite a summary of the series of structures given as input.


Compute BondsCompute atomic bonds.
Count BondsAdd as atom data the atom's number of bonds.
Count H BondsCount the number of H Bonds present in the input structure. The count is added to the structure global data.
Compute Selected BondsAdds bonds to specific atoms using a distance criteria.
Set Manual BondsManually add bonds between atoms.


Solvent Excluded SurfaceCompute the molecule Solvent Excluded Surface.
BackboneCompute a protein backbone.
General BackboneDisplay a tube through user selected atoms.
Vector GlyphDisplay with arrows the vector data associated with a given structure.
Merge ValuesAdd a new scalar or vector data to atoms, bonds or globally to the given structure.
Atoms Values TraspAtoms are rendered with transparency dependent on the associated scalar value
Particle DensityCompute the average particle mass density using uniform binning.
Interpolating PlaneBuild the least square plane interpolating a set of picked atoms (n ≥ 3).


Select AtomsSelect specific atoms.
Select FragmentsSelect specific structure fragments (i.e. residues).
Threshold DataSelect atoms whose associated scalar value meets various criteria.
Delete AtomsInteractively delete atoms.


Accumulate TracesAccumulate traces (accumulated positions) for specific atoms in a sequence of time steps.
Accumulate Global DataAccumulate a global scalar data in a form suitable for charting.
Interpolate SequenceLinearly interpolate a given number of positions between each pair of timesteps.
Velocity MeanCompute the average particle velocity using uniform binning.
Enthalpy TransitionsSearch a range of pressure values to find where the structure with the minimum enthalphy changes.


Replicate LatticeReplicate the structure unit cell along the three base vectors.
Apply SymmetriesCompute new atoms positions from the space group of the input molecule.
Shift Unit CellShift the unit cell to re-center periodic phenomena that are split between the opposite sides of the cell.
Enlarge Unit CellAdd atoms outside the unit cell by different criteria.
Move StructureTranslate and rotate a given structure modifying all the atoms coordinates.
Crop StructureCrop a structure and the optional volume data inside a given geometry.
Crop From PlaneRemove atoms that dist more than a given value from a plane.
Miller PlaneCrop the atoms using the plane identified by given Miller indices.
Draw PolyhedraDisplay a convex polyhedron around selected atoms.
Draw Simple PolyhedraDisplay a convex polyhedron around selected atoms using a different setup.
X Ray Structure FactorCompute and display simplified X-Ray structure factors.
Remove Border AtomsRemove atoms that bonds with atoms outside the unit cell.
Merge Unit CellApply the unit cell of one structure to another one.
Find SymmetriesFind symmetries in the input structure and simplify it.


IsosurfaceCreate an isosurface for a given scalar volumetric value.
OrthosliceCreate an orthoslice for a given scalar volumetric value.
Volume RenderVolumetric render of a scalar valued volume.
Cube on SurfaceAssign to a surface the values of the volume in which the surface is immersed in the positions occupied by the surface itself.
Cut SurfaceCut a surface (eg. a Solvent Excluded Surface) with a plane.
Bicolor SurfaceColor a surface on one side with a user specified color leaving the other one with its original coloring.
Interpolate VolumeInterpolate a given scalar volume adding points between original grid points.


Draw StructureTransform the molecule structure data into graphic objects for display.
Draw Sw StructureTransform the molecule structure data into graphic objects for display using a software render method.
Info Sets EditorManage, edit, create and destroy Info Sets.
Display Unit CellDisplays the borders of the unit cell.
Set Rendering ModeSet the rendering mode on an atom by atom base.
Axis GlyphDisplay three arrows to mark the origin and the XYZ axis directions, or the unit cell abc vectors. The glyph could also be offset from the origin.
Background FadeProvide a colored backdrop for which you can set the four corners colors.
LogoCreate a logo image to be added to a viewer. The image is locked in the viewer and is not transformed by standard mouse actions.
Enclosing EllipsoidCompute an ellipsoid that encloses the given set of atoms.
Time LegendDisplay a progress bar to show the current timestep / current time for an animated molecule trajectory.
Color LegendDisplay a legend for the structure representation colors.
Discrete LegendColor legend for integer values in an user specified range.
Smooth TubeCreate a tube that connect all the given points.
Error TubeCreate a tube with a radius proportional to the values associated to the connected points.
Structure InfoShow count of the number of atoms present in the input structure.

Probe and Measure

Measure StructureAccess information about and measure a displayed structure.
Measure Closer AtomsMeasure intra-atomic distances between a given atom and the surrounding ones in a given range.
Pick Unit CellRedefines the unit cell for the displayed structure by picking on four atoms.

Full Apps

MolDisplayAppRead and display a molecule.
CrystalDisplayAppRead and display structures with symmetries and unit cell replication.
VolumeDisplayAppRead and display a structure that has volumetric data associated.
PickDisplayAppRead and display a structure and enable picking to measure it.
TracesDisplayAppRead and display atom traces during a trajectory visualization.
TracesDisplaySwAppRead and display atom traces during a trajectory visualization (using sw rendering).
PickUnitCellAppRedefine the molecule unit cell by corner picking and crops the structure inside the new unit cell.
FermiSurfacesAppThis is a full application ready for use to display Fermi surfaces computed at a given Fermi energy.
FermiBandsAppThis is a full application ready for use to display energy for Fermi along a given polyline.

Datatype Definitions

MoleculeTypeDatatype used by the modules that operate on molecular data.
DisplayParamsTypeDatatype that carries information on how the molecules are rendered on screen.