CYANA Command: write upl: Difference between revisions

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== Parameters ==
== Parameters ==


; file=''filename''.upl
; file=''filename''.upl:(required)  
:(required) The name of the output upper distance limit file. The default filename extension ".upl" is used unless a filename extension is given explicitly.
;list=''integer'':(default: 1)
; sorted                         
;nmrstar=''integer'':(default: 2)
: Option to sort the distance restraints by the first and second atom. By default, the upper distance limits 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.
;details                       
; swapped                         
;multiple                     
: Option to output restraints that involve diastereotopic hydrogens or methyl groups after optimal swapping of the stereopartners for minimal target function value.
;sorted                         
; xplor  
;swapped                         
: Option to output the file in the format of the program XPLOR instead of the standard [[distance restraint file]] format of the program CYANA.                     
;xplor                        
; nocomments
;nocomments                    
: Option to suppress the output of comments such as the number of the peak from which the restraint originated.                   
;append
; append
: Option to append the output to the given file. By default, an already existing output file is overwritten.                       


== Description ==
== Description ==


Writes an upper limit distance restraint file. Optionally, the output
Writes an upper limit distance restraint file. Optionally, the output may be appended to an existing file.
may be appended to an existing file.


==== Ambiguous distance restraints ====


Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''&alpha;''<sub>1</sub>,''&beta;''<sub>1</sub>),...,(''&alpha;<sub>n</sub>'',''&beta;<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition


== Parameters ==
:<math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.


; file=''filename''.seq           
''d''(''&alpha;''<sub>i</sub>,''&beta;''<sub>i</sub>) is the distance between the atoms ''&alpha;''<sub>i</sub> and ''&beta;''<sub>i</sub>.  
:(required) The name of the output sequence file. The filename extension ".seq" is used unless a filename extension is given explicitly.
; pure
: Option to write purely the residue names and residue numbers, excluding possible ''cis''-peptide bond declarations or '''link''' statements.
; append
: Option to append the output to the given file. By default, an already existing output file is overwritten.


== Description ==
Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.


Writes a file with the currently selected upper distance limits in the standard [[distance restraint file]] format of the program CYANA.
==== Shorthand form ====


Instead of the command  
Instead of the command  


  write seq ''filename''.upl
  write upl ''filename''.upl


the shorthand version  
the shorthand version  
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  write ''filename''.upl
  write ''filename''.upl


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

Latest revision as of 12:11, 12 January 2010

Write upper distance limit file

Parameters

file=filename.upl
(required)
list=integer
(default: 1)
nmrstar=integer
(default: 2)
details
multiple
sorted
swapped
xplor
nocomments
append

Description

Writes an upper limit distance restraint file. Optionally, the output may be appended to an existing file.

Ambiguous distance restraints

Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with n assignments to atom pairs (α1,β1),...,(αn,βn) and an upper distance bound b imposes on the structure the condition

.

d(αi,βi) is the distance between the atoms αi and βi.

Note that the "effective distance" deff cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound b, regardless of the possible presence of other assignments that correspond to longer distances.

Shorthand form

Instead of the command 

write upl filename.upl

the shorthand version 

write filename.upl

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

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