Difference between revisions of "Tutorial"

From MSL-Libraries
Jump to navigationJump to search
 
(15 intermediate revisions by 2 users not shown)
Line 7: Line 7:
 
*** [[Tutorial:Getting started: Downloading MSL|Getting started: Downloading MSL]]
 
*** [[Tutorial:Getting started: Downloading MSL|Getting started: Downloading MSL]]
 
** ''Compiling''
 
** ''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 MSL with external libraries|Getting started: Compiling MSL with external libraries]]
 +
*** [[Tutorial:Getting started: Compiling MSL|Getting started: Compiling MSL without external libraries]]
 
*** [[Tutorial:Getting started: Compiling your own programs in MSL|Getting started: Compiling your own programs in MSL]]
 
*** [[Tutorial:Getting started: Compiling your own programs in MSL|Getting started: Compiling your own programs in MSL]]
 
+
** ''Developers - Checking In''
 +
*** [[Tutorial:Check in procedure]]
 +
* '''Download topology/parameter files'''
 +
** [[Tutorial: Download CHARMM topology and parameter files]]
 
* '''Molecular objects: atoms, residues, chains...'''
 
* '''Molecular objects: atoms, residues, chains...'''
 
** ''Read and write coordinates to/from files''
 
** ''Read and write coordinates to/from files''
Line 24: Line 27:
  
 
* '''Molecular Modifications, Movements and Computing Geometries'''
 
* '''Molecular Modifications, Movements and Computing Geometries'''
*** Measuring distances, angles, dihedrals
+
** [[Tutorial:Measuring distances, angles, dihedrals| Measuring distances, angles, dihedrals]]
*** Applying translations and rotations
+
** Applying translations and rotations
*** Changing conformation
+
** Changing conformation
*** [[Tutorial:Molecular alignments| Molecular (Structural) Alignments]]
+
** [[Tutorial:Molecular alignments| Molecular (Structural) Alignments]]
*** Generating coiled-coils
+
** [[Tutorial::CoiledCoils_Bundles| Generating Coiled-coils and Symmetric Bundles]]
*** Generating Symmetric Bundles
+
** Generating Fusion Proteins
*** Generating Fusion Proteins
+
** [[Tutorial::Mutating Residues|Mutating residues and adding additional conformations]]
*** Mutating Residues
 
  
 
* '''Calculating Molecular Properties and Energies'''
 
* '''Calculating Molecular Properties and Energies'''
 
** Calculating Solvent Exposed Surface Area
 
** Calculating Solvent Exposed Surface Area
 
** Calculating CHARMM Energies
 
** Calculating CHARMM Energies
 +
** Using Statistical Potentials in MSL
  
  
 
* '''Using MSL Supporting Classes'''
 
* '''Using MSL Supporting Classes'''
** Parse command line options
+
** [[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

Latest revision as of 21:30, 22 September 2013

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.

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




  • Interfacing with R
    • Calling R from within MSL (including passing data back and forth)
  • Cartesian Minimization
    • Minimization of a simple System of atoms