Data for CYANA structure calculations
-------------------------------------

16.12.2019


manual-manual	structure calculation with manually assigned chemical shifts
		and manually assigned NOESY peak lists
  Input files:
  sso7d.seq	  amino acid sequence
  sso7d.aco	  torsion angle restraints (from TALOS)
  sso7d.prot	  chemical shift list  <== PROVIDED BY USER
  N15NOESY.peaks  N15 NOESY peak list  <== PROVIDED BY USER 
  C13NOESY.peaks  C13 NOESY peak list (optional)
  ref.pdb	  reference structure (for comparison only)
  CALC.cya	  CYANA script to run structure calculation
  CALCupl.cya	  CYANA script to (re)run structure calculation from the 
		  upper distance limit file (sso7d.upl) instead of peak lists
  
  Command to start structure calculation:
  cyana -n 50 CALC
  
  Output files:
  sso7d.upl	  upper distance limits (created from NOESY peak lists)
  sso7d.pdb	  3D structure, 10 conformers
  sso7d.ovw	  structure calculation statistics: TF values, violations, RMSD
  CALC.out	  log-file of structure calculation


manual-noeassign  structure calculation with manually assigned chemical shifts
		  and automatically assigned NOESY peak lists
  Input files:
  sso7d.seq	  amino acid sequence
  sso7d.aco	  torsion angle restraints (from TALOS)
  sso7d.prot	  chemical shift list  <== PROVIDED BY USER
  N15NOESY.peaks  N15 NOESY peak list  <== PROVIDED BY USER 
  C13NOESY.peaks  C13 NOESY peak list
  ref.pdb	  reference structure (for comparison only)
  CALC.cya	  CYANA script to run NOE assignment & structure calculation
  
  Command to start structure calculation:
  cyana -n 50 CALC
  
  Output files:
  cycle*.*	  results from intermediate NOE assignment cycles 1-7
  final.upl	  upper distance limits (created from NOESY peak lists)
  final.pdb	  3D structure, 10 conformers
  final.ovw	  structure calculation statistics: TF values, violations, RMSD
  CALC.out	  log-file of structure calculation


flya-noeassign    structure calculation with automatically assigned chemical shifts
		  and automatically assigned NOESY peak lists
  Input files:
  sso7d.seq	  amino acid sequence
  sso7d.aco	  torsion angle restraints (from TALOS)
  ref.prot	  reference chemical shift list (for comparison only)
  ref.pdb	  reference structure (for comparison only)
  N15NOESY.peaks  N15 NOESY peak list  <== PROVIDED BY USER 
  *.peaks         peak lists from other spectra:
  CALCFLYA.cya	  CYANA script to run chemical shift assignment (FLYA)
  CALC.cya	  CYANA script to run NOE assignment & structure calculation
  
  Command to start automated shift assignment and structure calculation:
  cyana -n 20 CALCFLYA
  cyana -n 50 CALC         # after CALCFLYA has finished
  
  Output files:
  *_exp.peaks	  expected peaks for each spectrum
  *_asn.peaks     experimental peak lists with FLYA assignments
  flya.prot	  automatically determined chemical shift assignments
  flya.pdf	  overview figure with FLYA assignments
  flya.tab	  table of FLYA chemical shift assignments
  flya.txt        FLYA assignment statistics
  
  cycle*.*	  results from intermediate NOE assignment cycles 1-7
  final.upl	  upper distance limits (created from NOESY peak lists)
  final.pdb	  3D structure, 10 conformers
  final.ovw	  structure calculation statistics: TF values, violations, RMSD
  CALC.out	  log-file of structure calculation
