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 executes the commands in the initialization macro 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 the CALC.cya macro file (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

demo.pdb.

The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard simulated annealing schedule with 4000 torsion angle dynamics steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file demo.pdb, and an overview table is saved in the file demo.ovw:

   Structural statistics:

   str   target     upper limits    van der Waals   torsion angles
       function   #    rms   max   #    sum   max   #    rms   max
     1     1.56   1 0.0073  0.36   5    5.2  0.34   0 0.3460  3.19
     2     1.87   2 0.0084  0.36   5    6.1  0.33   0 0.3813  3.63
     3     1.92   2 0.0083  0.36   5    5.8  0.36   0 0.3491  3.29
     4     1.94   1 0.0082  0.36   6    6.4  0.34   0 0.3478  3.46
     5     2.02   2 0.0080  0.35   7    5.7  0.34   0 0.5790  4.35
     6     2.05   1 0.0082  0.35   8    6.0  0.34   0 0.5704  4.29
     7     2.12   2 0.0092  0.36   4    6.5  0.35   0 0.3629  3.47
     8     2.20   4 0.0105  0.36   5    7.2  0.31   0 0.3597  3.45
     9     2.24   2 0.0087  0.36   6    7.4  0.34   0 0.3843  3.47
    10     2.34   3 0.0119  0.61   5    6.6  0.35   0 0.3309  3.05

   Ave     2.03   2 0.0089  0.38   6    6.3  0.34   0 0.4011  3.56
   +/-     0.21   1 0.0013  0.08   1    0.7  0.01   0 0.0881  0.41
   Min     1.56   1 0.0073  0.35   4    5.2  0.31   0 0.3309  3.05
   Max     2.34   4 0.0119  0.61   8    7.4  0.36   0 0.5790  4.35
   Cut                      0.20             0.20             5.00

   Constraints violated in 3 or more structures:
                                                  #   mean   max.  1   5   10
   Upper HA    ASP   68 - H     ASN   69   3.28   4   0.11   0.29   +*   ++    peak 1162
   Upper HB    ILE   85 - H     ASP   86   3.80  10   0.36   0.36  +++++++++*  peak 803
   VdW   N     LEU   39 - CD1   LEU   39   3.05  10   0.23   0.24  ++++++++*+
   VdW   N     ILE   81 - CD    PRO   82   3.05  10   0.26   0.28  ++*+++++++
   VdW   N     ILE   81 - HD2   PRO   82   2.45  10   0.34   0.36  ++*+++++++
   VdW   CG2   ILE   81 - C     ILE   81   2.90   6   0.20   0.22  ++  ++ *+
   VdW   CB    THR   91 - H     GLN   92   2.55   7   0.22   0.27  ++++++   *
   VdW   O     THR   91 - CB    GLN   92   2.90   3   0.15   0.20       * ++
   VdW   HA    VAL  107 - CD    PRO  108   2.60   4   0.18   0.30    *+  + +
   2 violated distance restraints.
   7 violated van der Waals restraints.
   0 violated angle restraints.

   RMSDs for residues 10..100:
   Average backbone RMSD to mean   :    0.52 +/- 0.09 A (0.40..0.72 A; 10 structures)
   Average heavy atom RMSD to mean :    1.04 +/- 0.06 A (0.96..1.17 A; 10 structures)