Page History

Content

• 1 CYANA setup
  
• 2 Automated resonance assignment
  • 2.1 Experimental input data
    • 2.1.1 SPECTRUM definitions in the CYANA library
  • 2.2 Exercise 1: Determine the spectrum type
  • 2.3 Exercise 2: Run FLYA
    • 2.3.1 Execution scripts or "macros" in CYANA
    • 2.3.2 The init macro
    • 2.3.3 The FLYA CALC macro
  • 2.4 FLYA output files
    • 2.4.1 The flya.txt file
    • 2.4.2 The flya.tab file
    • 2.4.3 The flya.pdf file
  • 2.5 Exercise 3: Analyze the FLYA results
• 3 Using Talos to generate torsion angle restraints
  • 3.1 Exercise 4: Calculate backbone torsion angle restraints using Talos
• 4 Automated NOESY assignment and structure calculation
  • 4.1 Exercise 5: Run noeassign
    • 4.1.1 The noeassign CALC macro
• 5 Creating the ligand library file for CYANA
  • 5.1 Exercise 6: Drawing the molecule and obtaining the SMILES code
  • 5.2 Exercise 7: Converting the SMILES code to mol2
  • 5.3 Exercise 8: Converting the mol2 file to a lib file for CYANA
  • 5.4 Alternative Exercise 6-8: Converting a pdb file to a lib file for CYANA
• 6 Calculating the structure of the protein-ligand complex
  • 6.1 Exercise 9: (Semi-automatic) Intermolecular cross peaks assignment and structure calculation
• 7 Comparing the calculated NMR structure to an XRAY reference structure
  • 7.1 Exercise 10: Compare the NMR structure to the Xray structure
  • 7.2 Exercise 11: Preparing an xray structure to use within CYANA
  • 7.3 Exercise 12: Calclulate the RMSD of NMR vs. xray structure using a CYANA macro
• 8 Beyond The Basics: Improving the final structure
  • 8.1 FLYA options
  • 8.2 neoassign options
  • 8.3 Exercise 13: Mapping restraints onto a known structure
  • 8.4 Exercise 14: Work on improving the final structure