Tutorials

Example calculations

• Download [[Media:Cyana-3.0-demo.zip|input data files] for example calculations.

• Basic structure calculation starting from given restraints
• Structure calculation using manually assigned NOESY peak lists
• Structure calculation with automated NOESY assignment
• Homodimer structure calculation with automated NOESY assignment
• Structure calculations using residual dipolar coupling restraints
• Structure calculations using pseudocontact shift restraints
• Various additional tasks
  • Analyze a structure
  • Angle restraints based on CA chemical shifts
  • Create restraints for disulfide bonds
  • Systematic local conformation analysis
  • Create restraints for hydrogen bonds
  • Merge multiple restraints files
  • Migrate data from Cyana 1.x or Dyana
  • Migrate data from Xplor or CNS
  • Modify upper distance limits
  • NOE statistics and plots
  • Prepare files for PDB and BMRB deposition
  • Create restraints to close flexible PRO rings
  • Ramachandran plot and rotamer restraints
  • Renumber chemical shifts and peaks
  • Calculate RMSD values and mean structures
  • Angle restraints from the program TALOS

Input file formats

• Residue library file (.lib)
• Sequence file (.seq)
• Distance restraint file (.upl, .lol)
• Torsion angle restraint file (.aco)
• Residual dipolar coupling restraint file (.rdc)
• Pseudocontact shift restraint file (.pcs)
• DG Cartesian coordinate file (.cor)
• PDB coordinate file (.pdb)
• Torsion angle file (.ang)
• XEASY chemical shift list file (.prot)
• BMRB chemical shift list file (.bmrb)
• XEASY peak list file (.peaks)
• NMRView peak list file (.xpk)