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Spectrum

XML Spectrum description (version 2.3)

Presentation

 

In ARIA, a spectrum is an xml file containing a peak list. The spectrum file is an output of the conversion

step.

 

List of attributes

 

The list of attributes is:

  • 'name' is the name of the spectrum given in the xml input file for conversion.
  • 'number' is the peak id. This peak number is used (with the name ref_no) in the files noe_restraints.*, which are the output of violations analysis.
  • 'reliable' defines whether the peak can be removed from the sets of peaks which can be assigned: the value 'no' means that the peak can be  removed, the value 'yes' that it is not possible.
  • 'volume' is the peak volume, 'error' the error on the volume. 'intensity' is the peak intensity with error. Either volume or intensity is used, and this is monitored in the Project xml file.
  • 'shift' are the hydrogen or heteronucleus chemical shifts of the peak
  • The chemical shifts present in the elements 'proton1', 'proton2', 'hetero1' and 'hetero2' are determined according to the 'proton1', 'proton2', 'hetero1', 'hetero2' attributes in the conversion input file.

 

Example of file

 

An example of spectrum xml file is given below:

 

<!DOCTYPE spectrum SYSTEM "noesy_spectrum1.0.dtd">
<spectrum name="15N NOESY">
  <peak number="1" reliable="no">
    <volume value="256000.0" error="0.0"/>
    <intensity value="" error=""/>
    <proton1>
      <shift value="8.875" error=""/>
      <assignment>
        <atom segid="    " residue="10" name="H"/>
      </assignment>
    </proton1>
    <proton2>
      <shift value="8.875" error=""/>
      <assignment>
        <atom segid="    " residue="10" name="H"/>
      </assignment>
    </proton2>
    <hetero1>
      <shift value="119.917" error=""/>
      <assignment>
        <atom segid="    " residue="10" name="N"/>
      </assignment>
    </hetero1>
    <hetero2>
      <shift value="" error=""/>
    </hetero2>
  </peak>
.....................

 

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