CNS language tutorials:

• CNS language
  • CNS scripting language
  • Specifying vectors and matrices
• Selections and operations
  • Selecting atoms - the basics
  • Selecting and operating on atomic properties
  • Selecting structure factors - the basics

Coordinate and topology tutorials:

• Creation of topology and parameter files
  • Making topology files
  • Making parameter files
  • Learning parameters from coordinates
  • N-terminal acetyl and C-terminal amide capping groups
  • Tools for building coordinates of hetero compounds
  • Distributed topology and parameter files
• Generating PDB and MTF files
  • The term "generate" explained
  • Generating and manipulating the molecular topology
  • A simple protein
  • A protein with a ligand and an ion
  • A protein with capping groups + ion + water
  • A simple DNA duplex
  • A simple RNA duplex
  • A hybrid DNA/RNA duplex
  • A protein + DNA + ions + water
• Coordinate manipulation
  • Manual coordinate manipulation
  • Generating the full molecule from a protomer

Crystallographic tutorials:

• Data conversion
  • Converting a scalepack reflection file
  • Converting a CCP4 MTZ reflection file
• Phasing by Multiple Anomalous Diffraction (MAD)
  • Flowchart of MAD phasing protocol (PDF format)
  • Guidelines for MAD phasing protocol
  • Preparation of diffraction data
  • Intensity statistics
  • Anomalous difference Patterson map
  • Heavy-atom search
  • Heavy-atom refinement/MAD phasing
  • Resolution of the enantiomorph ambiguity
  • Completion of the heavy-atom model
  • Phase improvement by density modification
• Phasing by Single Anomalous Diffraction (SAD)
  • Flowchart of SAD phasing protocol (PDF format)
  • Guidelines for SAD phasing protocol
  • Preparation of diffraction data
  • Intensity statistics
  • Anomalous difference Patterson map
  • Heavy-atom search
  • Heavy-atom refinement/SAD phasing
  • Completion of the heavy-atom model
  • SAD Phasing - Density Modification - Selection of Map
• Phasing by Isomorphous Replacement (SIR/MIR)
  • Flowchart of SIR/MIR phasing protocol (PDF format)
  • Preparation of diffraction data
  • Intensity statistics
  • Isomorphous difference Patterson map
  • Heavy-atom search
  • Initial SIR phasing
  • Locating sites in other derivatives followed by MIR phasing
  • Completion of the heavy-atom model
  • Phase improvement by density modification
• Phasing by Molecular Replacement
  • Flowchart of MR phasing protocol (PDF format)
  • Generating the search molecule
  • Cross-rotation search to determine rotation
  • Translation search to determine translation
  • Translation search with a fixed molecule to complete dimer
  • Adding cross-validation information to the reflection file
  • Rigid-body refinement of the solution
  • Calculating a cross-validated sigma-A weighted electron density map
  • Reducing model bias with the composite omit map
  • Reducing model bias by density modification
• Structure refinement with experimental phases
  • Preparation of diffraction data
  • Generating the initial model
  • Checking the initial model
  • Initial refinement by simulated annealing
  • Locating missing parts of the model
  • Rebuilding followed by refinement
  • Automatically locating water molecules
  • Checking the model statistics and maps
• Structure refinement without experimental phases
  • Preparation of diffraction data
  • Generating the initial model
  • Checking the initial model
  • Initial refinement by simulated annealing
  • Locating missing parts of the model
  • Rebuilding followed by refinement
  • Automatically locating water molecules
  • Checking the model statistics and maps
• Structure refinement with hemihedral twinning
  • Detection of twinning
  • Preparation of diffraction data
  • Checking the initial model
  • Refinement by simulated annealing
  • Automatically locating water molecules
  • Checking the model statistics and maps
• The use of non-crystallography symmetry (NCS)
  • Strict NCS (constraints) in refinement
  • NCS restraints in refinement

NMR tutorials:

• Initial template generation
  • Generating the molecular topology
  • Generating initial extended coordinates
• Structure calculation
  • Simulated annealing
  • Distance geometry simulated annealing

Formats:

• HTML interface
  • CNS task file syntax
• Coordinates
  • CNS coordinate files
• Crystallographic
  • Reflection files
  • Electron density maps
  • Masks
• NMR
  • Distance restraints
  • Dihedral angle restraints

Other information:

• Notes on ambiguities encountered in phasing

    run_tutorial

    cns_solve < water_pick.inp > water_pick.out [6.5 minutes]