CYANA Macro: opalprefine

Parameters

omegawidth=real

(default: 0.1)

opalp=string

(default: opalp)

opalptable=string

(default: opalptable)

cofima=string

(default: cofima)

coco=string

(default: none)

refine=string

(default: refine)

Description

Performs restrained energy refinement of the current structures using the external program OPALp, its supporting script opalptable, and the auxiliary external programs COFIMA and COCO. OPALp (Koradi et al., 2000; Luginbühl et al., 1996) is a program for energy minimization and molecular dynamics simulation in Cartesian space that uses the AMBER force field (Cornell et al., 1995). COFIMA is a program for coordinate and restraint file manipulation, and COCO compares the covalent geometry – bond lengths, bond angles, fixed distances, RMSDs for rigid units, and fixed (improper) torsion angles – of a structure with standard values. OPALp and the auxiliary programs are not part of CYANA and must be installed separately. The pathnames of these programs can be set by the corresponding parameters, and the name of the OPALp command that will be used for the restrained energy refinement of each individual structure is given by the refine parameter.
Restrained energy refinement in Cartesian space is performed by OPALp for all selected structures using the current distance and torsion angle restraints. The opalprefine command performs the necessary format conversions, runs the external program OPALp, and analyzes the results. The omega torsion angles are restrained during the energy refinement by torsion angle restraints centered at 180°±omegawidth or 0°±omegawidth, if omegawidth is positive. The output files of a restrained energy refinement with the opalprefine command comprise: The final structure calculation produces the following files:

Energies

Overview of energies, restraint violations, hydrogen bonds, Ramachandran plot quality, RMSDs etc. before and after energy refinement.

opalp.pdb

Output structure after restrained energy-refinement with OPALp, converted back to CYANA nomenclature

cyana-mean.pdb

Mean coordinates of the cyana.pdb structure, obtained after optimal superposition of the conformers in cyana.pdb for minimal RMSD for the backbone atoms of the residues specified by the variable rmsdrange, or all residues by default.

opalp-mean.pdb

Mean coordinates of the opalp.pdb structure.

ramacyana.ps

Ramachandran plot for the input structure

ramaopalp.ps

Ramachandran plot for the energy-refined structure obtained from OPALp

coco.out

Results of the covalent geometry checks performed by the external program COCO (only if the coco parameter was given)

cyana.aco

Copy of the input torsion angle restraints

cyana.pdb

Copy of the input structure

opalp.upl

Upper distance bound restraints used by OPALp

opalp.lol

Lower distance bound restraints used by OPALp, if any

opalp.aco

Torsion angle restraints used by OPALp, if any