Masayo: /* Description */

2009-08-06T13:03:23Z

Description

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	== Description ==		== 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.<br>
			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

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2009-01-29T11:26:59Z

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== 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 ==

CYANA Macro: opalprefine - Revision history

Masayo: /* Description */

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