CYANA 3.0 Reference Manual

INCLAN (INteractive Command LANguage)

• INCLAN Reference Manual

CYANA Scripts

• cyanaclean
• cyana
• cyanafilter
• cyanajob
• cyanatable

CYANA Commands

• CYANA Commands (complete list)

CYANA Functions

• CYANA functions (complete list)

CYANA Variables

• CYANA variables (complete list)

Selections

• Selection rules

• Atom selection
• Angle selection
• Peak selection
• Distance restraint selection
• Scalar coupling selection
• Residual dipolar coupling selection
• Pseudocontact shift selection
• Structure selection

Input files

• 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)

Algorithms

• Standard nomenclature for amino acids and nucleotides

Algorithms

• Coordinate generation
• Target function
• Torsion angle dynamics
• Momenta compensation
• Simulated annealing