CYANA Macro: overview
Parameters
- file=filename.ovw
- (default: none)
- structures=integer
- (default: 0)
- range=string
- (default: none)
- reference=string
- (default: none)
- significant=integer
- (default: -1)
- hbond=integer
- (default: -1)
- mode=sum|average|rms
- (default: rms)
- ang
- cor
- pdb
- mean
- details
Description
Sorts the selected structures with regard to their target function value and creates an overview file name.ovw for the first n of these structures. If the name parameter is not specified and if a variable with name name is defined, then its value is used as name. Pair-wise RMSDs are calculated for the given residue range (see command rmsd). The RMSD calculation can be suppressed by setting range=-. If the range parameter is not specified and if a variable with name rmsdrange is defined, then its value is used as residue range. Optionally, output angle (ang), DG coordinate (cor) or PDB coordinate (pdb) files of the structures may be written with file names "name.ang", "name.cor" or "name.pdb", respectively. The structures may be analyzed for hydrogen bonds (option hbond), or for violations of steric lower distance limits (option vdw). Note: Because the target function is re-calculated, it is important that all restraints used for the calculation of the structures are present and that the same weights are used. An overview file may contain four different tables:
For each structure: the target function value, the numbers, sums and
maxima of restraint violations (the output of the structure list command).
For each violated restraint: the structures in which it is violated by
more than the corresponding cutoff value (the output of the structure violate command). By default, violations are shown only if they occur in at least one third of the conformers. To obtain a listing of all violations larger than the cutoffs, the option full must be set.
For all pairs of structures: the RMSD for the backbone and all heavy
atoms (output of the rmsd command). By default only the average value of all pairwise comparisons is written. A table with the individual pairwise RMSD values is created only if the option full is set.