Return to Main Documents Page

SASSIE

There are several sections in the SASSIE main GUI menu. Each of these sections contains a set of related modules that carry out similar or related tasks. A list of each section and a list of associated modules with a brief description of each is shown below. A few modules are not available for general use and are depicted as "ALPHA".

Tools -- general utilities

Contrast Calculator Experimental planning to predict scattering length density and I(0) from input PDB file, Fasta sequence file, or chemical formula.

Align Moves structures from input structure file so that they overlap with a reference input structure.

Data Interpolation Creates a new data file that is spaced in a uniform grid from input experimental data file.

Extract Utilities Allows user to extract individual structures and/or SAS profiles from a larger input structure file and/or folder containing SAS profiles.

Merge Utilities Allows user to combine user supplied structures and calculated scattering profiles into a single set of new files.

Build -- evaluate and clean up structure files

Build Utilities Methods to modify PDB files and structures to hlep build starting structures for modeling. (BETA)

PDB Scan Generates a report that characterizes the user supplied PDB file.

PDB Rx Attempts to correct mistakes in user supplied PDB file (ALPHA).

CG Builder Tools to assist the generation of coarse-grain structures (ALPHA).

Interact -- visualize and manipulate structures

Molecular Viewer Interactive display of three-dimensional coordinates from user supplied PDB file using JSMol.

Interactive SAS Interactive display of three-dimensional coordinates from user supplied PDB file using JSMol and simultaneous display of X-ray or neutron scattering profiles (ALPHA).

Simulate -- create trajectories from a starting structure

Monomer Monte Carlo Performs molecular Monte Carlo simulation of single chain protein and nucleic acids.

Complex Monte Carlo Performs molecular Monte Carlo simulation of multiple chain protein and single chain nucleic acids.

Torsion Angle Monte Carlo Performs molecular Monte Carlo simulation of proteins, single stranded nucleic acids, double stranded nucleic acids, some carbohydrates and selected polymers (BETA).

Energy Minimization Performs energy minimization and molecular dynamics simulation of input structures.

Torsion Angle MD Performs torsion-angle molecular dynamics of proteins, nucleic acids, carbohydrates and their complexes of input structures.

ProDy Generates structures by performing molecular normal mode analysis of input structure using the open-source molecular dynamics package ProDy.

Docking Generates structures by performing molecular docking based on surface similarity. (ALPHA)

Two-Body Grid Generates structures by sampling by rigid body displacements.

Calculate -- generate theoretical scattering data from structures

SasCalc Calculates neutron and X-ray scattering profiles from all-atom input structures.

Xtal2sas Calculates neutron scattering profiles from input structures. (RETIRED)

Cryson Calculates neutron scattering profiles from input structures. (RETIRED)

Crysol Calculates X-ray scattering profiles from input structures.

SCT Calculate Calculates neutron and X-ray scattering profiles from input structures. (RETIRED)

SLD MOL Calculates neutron and X-ray reflectivity scattering length density from user supplied structures. Utilities for experimental planning and isotopic labeling and optimization of ensemble populations are supplied.

EM to SANS Calculates neutron scattering profile from user supplied electron density map.

Capriqorn Calculates X-ray scattering profiles from MD trajectories with explicit water. (ALPHA)

SasCalc-PBC Calculates neutron and X-ray scattering profiles from MD trajectories with periodic boundary conditions. (ALPHA)

Analyze -- compare theoretical data to experimental data and advanced analysis methods

Chi-Square Filter Compares calculated scattering profiles to user supplied interpolated scattering profiles. No fitting.

SCT Analyze Compares calculated scattering profiles to user supplied interpolated scattering profiles. No fitting. (RETIRED)

Density Plot Calculates volumetric gaussian cube files from user supplied structures. These files can be rendered in VMD and Pymol.

APBS Calculates non-polar solvation energy using adaptive Poisson-Boltzman solver from user supplied structures.

Return to Main Documents Page

Go to top