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=== 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 [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/ examples/] subdirectory. Previous knowledge of C++ is assumed. * '''Getting started''' ** ''Getting MSL'' *** [[Tutorial:Getting started: Downloading MSL|Getting started: Downloading MSL]] ** ''Compiling'' *** [[Tutorial:Getting started: Compiling MSL|Getting started: Compiling MSL]] *** [[Tutorial:Getting started: Compiling MSL with external libraries|Getting started: Compiling MSL with external libraries]] *** [[Tutorial:Getting started: Compiling your own programs in MSL|Getting started: Compiling your own programs in MSL]] * '''Molecular objects: atoms, residues, chains...''' ** ''Read and write coordinates to/from files'' *** [[Tutorial:Reading a PDB file with the simpler molecular object: the AtomContainer | Reading a PDB file with the simpler molecular object: the AtomContainer]] *** [[Tutorial:Reading a PDB file with the complex molecular object: the System | Reading a PDB file with the complex molecular object: the System]] ** ''Interacting and manipulating molecular objects'' *** [[Tutorial:Looping over Chains, Residues, Atoms in the System| Looping over Chains, Residues, Atoms in the System]] *** Getting Chains, Residues, Atoms by id <!-- *** [[Tutorial:Molecular Object Getters | Checking for existance of Atoms, Residues, Chains and getting them]] --> *** [[Tutorial:Passing atoms between objects: the AtomPointerVector | Passing atoms between objects: the AtomPointerVector]] *** [[Tutorial:Selecting subsets of atoms|Selecting subsets of atoms]] *** [[Tutorial:Using regular expression: Selecting sequence motifs of a Chain|Using regular expression: Getting parts of a structure that match a sequence motif ]] * '''Molecular Modifications, Movements and Computing Geometries''' ** [[Tutorial:Measuring distances, angles, dihedrals| Measuring distances, angles, dihedrals]] ** Applying translations and rotations ** Changing conformation ** [[Tutorial:Molecular alignments| Molecular (Structural) Alignments]] ** [[Tutorial::CoiledCoils_Bundles| Generating Coiled-coils and Symmetric Bundles]] ** Generating Fusion Proteins ** Mutating Residues * '''Calculating Molecular Properties and Energies''' ** Calculating Solvent Exposed Surface Area ** Calculating CHARMM Energies ** Using Statistical Potentials in MSL * '''Using MSL Supporting Classes''' ** [[Tutorial:OptionParser|Parse command line options]] * '''Interfacing with PyMOL''' ** Using the '''[[MSL Objects:PyMolVisualization|PyMolVisualization object]]''' to write out PyMOL script files ** Using the '''[[MSL Objects:PythonMSL|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

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