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
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)