Basic structure calculation starting from given restraints

This calculation shows how to calculate a structure from previously assigned upper limits. The input data are in the subdirectory ‘basic’ of the demo data zip archive:

demo.seq

amino acid sequence

demo.upl

upper distance limit restraints

demo.aco

dihedral angle restraints

init.cya

initialization macro

CALC.cya

macro for the structure calculation

When CYANA is started, it automatically looks for the file init.cya, which usually holds basic setup for the calculations, e.g., reading the amino acid library and the amino acid sequence of the protein, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into CALC.cya (or even given on the command line), but as they are rarely changed for a given project, it is convenient have them in the init.cya file:

 rmsdrange:=10-100                     # define residue range for RMSD calculations
 cyanalib                              # read standard CYANA residue library 
 read seq demo.seq                     # read amino acid sequence

The actual structure calculation is performed by the commands in the macro file CALC.cya:

 read upl demo.upl			# read upper distance bounds
 read aco demo.aco			# read dihedral angle restraints
 
 calc_all 50 steps=4000		# calculate conformers
 
 overview demo.ovw structures=10 pdb	# analyze and write best conformers