Tutorials

Downloads

• Latest demo version of CYANA 3.0beta for Linux and Mac OSX (24.10.2012)
  The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.
  The regular CYANA version 3.0 is not released yet.
• Latest demo version of CYANA 3.96beta for Linux and Mac OSX (19.07.2013)
  The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.
  The regular CYANA version 3.96 is not released yet.
• Input data files for example calculations with CYANA 3.0 (also included with the demo version of CYANA). Not all of the demos are working with CYANA 2.1 or earlier.

INCLAN Tutorials

• Writing and using INCLAN macros
• Using INCLAN variables
• Using INCLAN control statements

CYANA Tutorials

• Automated resonance assignment with FLYA (EMBO Practical Course NMR in Basel, 20–27 July 2013)
• Defining non-standard residues

CYANA 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)