CYANA Command: write aco: Difference between revisions
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''Write torsion angle restraints'' | |||
== Parameters == | == Parameters == | ||
; file=''filename''.aco | ; file=''filename''.aco | ||
; redac | :(required) The name of the output torsion angle restraint file. The default filename extension ".upl" is used unless a filename extension is given explicitly. | ||
; xplor | ; redac | ||
; structures=''integer'': (default: 10) | : Option to derive redundant dihedral angle restraints for the REDAC strategy [http://dx.doi.org/10.1007/BF02192866 (Güntert & Wüthrich, 1991)]. See description below. | ||
; maxwidth=''real'': (default: 270.0) | ; xplor | ||
: Option to output the file in the format of the program XPLOR instead of the standard [[angle restraint file]] format of the program CYANA. | |||
; structures=''integer'' | |||
: (default: 10) The minimal number of structures in which the local target function of a residue and its immediate sequential neighbors must be below the value of the [[CYANA Variable: ang_cut|ang_cut]] to generate a dihedral angle restraint for the REDAC strategy. This parameter can only be used in conjunction with the '''redac'' option. | |||
; maxwidth=''real'' | |||
: (default: 270.0 degrees) The maximal width of the allowed range of a dihedral angle restraint for the REDAC strategy. This parameter can only be used in conjunction with the '''redac'' option. | |||
; append | ; append | ||
: Option to append the output to the given file. By default, an already existing output file is overwritten. | |||
== Description == | == Description == | ||
Writes | Writes a file with the currently torsion angle restraints in the standard torsion [[angle restraint file]] format of the program CYANA, or optionally in XPLOR format. | ||
Optionally, redundant dihedral angle restraints | |||
for the Redac strategy (Guentert & Wuethrich, 1991) may be derived | for the Redac strategy (Guentert & Wuethrich, 1991) may be derived | ||
from the current angle statistics and included in the output (option | from the current angle statistics and included in the output (option | ||
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redundant dihedral angle restraints for a given residue, its local | redundant dihedral angle restraints for a given residue, its local | ||
target function value (and that of its immediate neighbors must be | target function value (and that of its immediate neighbors must be | ||
below the cutoff value given by the variable ang_cut in at least N | below the cutoff value given by the variable [CYANA Variable: ang_cut|ang_cut] in at least N | ||
structures. Redundant dihedral angle restraints with an allowed range | structures. Redundant dihedral angle restraints with an allowed range | ||
wider than Df degrees are discarded. The parameters structures and | wider than Df degrees are discarded. The parameters structures and | ||
maxwidth can only be in conjunction with the redac option. | maxwidth can only be in conjunction with the redac option. | ||
Instead of the command | |||
write aco ''filename''.aco | |||
the shorthand version | |||
write ''filename''.aco | |||
can be used if the filename extension is ".aco". | |||
Latest revision as of 23:12, 3 February 2009
Write torsion angle restraints
Parameters
- file=filename.aco
- (required) The name of the output torsion angle restraint file. The default filename extension ".upl" is used unless a filename extension is given explicitly.
- redac
- Option to derive redundant dihedral angle restraints for the REDAC strategy (Güntert & Wüthrich, 1991). See description below.
- xplor
- Option to output the file in the format of the program XPLOR instead of the standard angle restraint file format of the program CYANA.
- structures=integer
- (default: 10) The minimal number of structures in which the local target function of a residue and its immediate sequential neighbors must be below the value of the ang_cut to generate a dihedral angle restraint for the REDAC strategy. This parameter can only be used in conjunction with the 'redac option.
- maxwidth=real
- (default: 270.0 degrees) The maximal width of the allowed range of a dihedral angle restraint for the REDAC strategy. This parameter can only be used in conjunction with the 'redac option.
- append
- Option to append the output to the given file. By default, an already existing output file is overwritten.
Description
Writes a file with the currently torsion angle restraints in the standard torsion angle restraint file format of the program CYANA, or optionally in XPLOR format.
Optionally, redundant dihedral angle restraints for the Redac strategy (Guentert & Wuethrich, 1991) may be derived from the current angle statistics and included in the output (option redac; see the commands angstat make and redac). In order to generate redundant dihedral angle restraints for a given residue, its local target function value (and that of its immediate neighbors must be below the cutoff value given by the variable [CYANA Variable: ang_cut|ang_cut] in at least N structures. Redundant dihedral angle restraints with an allowed range wider than Df degrees are discarded. The parameters structures and maxwidth can only be in conjunction with the redac option.
Instead of the command
write aco filename.aco
the shorthand version
write filename.aco
can be used if the filename extension is ".aco".