Tutorial

NOTE: the tutorial is under construction

The tutorial is a collection of articles that illustrate specific features of MSL. Each article explains example programs found in the examples/ subdirectory. Previous knowledge of C++ is assumed.

• Getting started
  • Getting MSL
    • Getting started: Downloading MSL
  • Compiling
    • Getting started: Compiling MSL
    • Getting started: Compiling MSL with external libraries
    • Getting started: Compiling your own programs in MSL
• Download topology/parameter files
  • Tutorial: Download CHARMM topology and parameter files
• Molecular objects: atoms, residues, chains...
  • Read and write coordinates to/from files
    • Reading a PDB file with the simpler molecular object: the AtomContainer
    • Reading a PDB file with the complex molecular object: the System
  • Interacting and manipulating molecular objects
    • Looping over Chains, Residues, Atoms in the System
    • Getting Chains, Residues, Atoms by id
    • Passing atoms between objects: the AtomPointerVector
    • Selecting subsets of atoms
    • Using regular expression: Getting parts of a structure that match a sequence motif

• Molecular Modifications, Movements and Computing Geometries
  • Measuring distances, angles, dihedrals
  • Applying translations and rotations
  • Changing conformation
  • Molecular (Structural) Alignments
  • Generating Coiled-coils and Symmetric Bundles
  • Generating Fusion Proteins
  • Mutating residues and adding additional conformations

• Calculating Molecular Properties and Energies
  • Calculating Solvent Exposed Surface Area
  • Calculating CHARMM Energies
  • Using Statistical Potentials in MSL

• Using MSL Supporting Classes
  • Parse command line options

• Interfacing with PyMOL
  • Using the PyMolVisualization object to write out PyMOL script files
  • Using the PythonMSL object to call MSL from within PyMOL

• Interfacing with R
  • Calling R from within MSL (including passing data back and forth)

• Cartesian Minimization
  • Minimization of a simple System of atoms