CYANA Command: write aco: Difference between revisions

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:(required) The name of the output torsion angle restraint file. The default filename extension ".upl" is used unless a filename extension is given explicitly.
:(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  
; redac  
: Option to derive redundant dihedral angle restraints for the REDAC strategy [http://dx.doi.org/10.1007/BF02192866 (Guntert & Wuthrich, 1991)]. See description below.                   
: Option to derive redundant dihedral angle restraints for the REDAC strategy [http://dx.doi.org/10.1007/BF02192866 (Güntert & Wüthrich, 1991)]. See description below.                   
; xplor     
; 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.                         
: 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''
; structures=''integer''
: (default: 10)
: (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)
; 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 an angle restraint file. Optionally, the output may be appended
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.  
to an existing file. Optionally, redundant dihedral angle restraints
 
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.
''Write upper distance limit file''
== Parameters ==
; file=''filename''.upl
:(required) The name of the output upper distance limit file. The default filename extension ".upl" is used unless a filename extension is given explicitly.
; sorted                       
: Option to sort the distance restraints by the first and second atom. By default, the distance restraints are written in the order in which they are stored in the program, e.g. the order in which they have been read from an input file.
; swapped                       
: Option to output restraints that involve diastereotopic hydrogens or methyl groups after optimal swapping of the stereopartners for minimal target function value.
; xplor   
: Option to output the file in the format of the program XPLOR instead of the standard [[distance restraint file]] format of the program CYANA.                     
; nocomments
: Option to suppress the output of comments such as the number of the peak from which the restraint originated.                   
; 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 selected upper distance limits in the standard [[distance restraint file]] format of the program CYANA, or optionally in XPLOR format.


Instead of the command  
Instead of the command  


  write upl ''filename''.upl
  write aco ''filename''.aco


the shorthand version  
the shorthand version  


  write ''filename''.upl
  write ''filename''.aco


can be used if the filename extension is ".upl".
can be used if the filename extension is ".aco".

Latest revision as of 00:12, 4 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".

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