Contents

• Introduction
• Installation
  • Compilation of the CNS program
  • Installation of Python
  • Downloading ARIA
  • Installing the cgi scripts on your server
  • editing your shell rc files
  • Setting up ssh to run ARIA on several machines
  • WHATCHECK, PROCHECK, PROSA
  
  
• Tutorial
  • Introduction
  • Getting started
    • Setting up a new project
    • Start ARIA within a UNIX shell
    • Editing the parmeters in run.cns
    • Start ARIA within a UNIX shell
  • Input files
  • Output files
  
  
• Data format
  • ARIA NOE peak files (.list suffix)
  • CNS files (.tbl suffix)
  • BioMagResBank support
  • XML support
  • Python modules for manipulating the data
  
  
• Description of ARIA protocols
  • Overview
  • setup of run directory tree
  • run.cns
  • generate.inp
  • generate_template.inp
  • stereoassign.cns
  • Sorting of structures
  • merge.inp
  
  
• Analysis protocols
  • Overview
  • PDB header
  • calib.inp
  • print_noe.inp
  • print_dih.inp
  • print_coup.inp
  • print_geom.inp
  • cop.inp
  • rmsave.inp
  • wellordered.inp
  
  
• Appendix - CNS scripting language
  • General features
  • Symbol definitions and the EVALuate statement
  • Parameter definition with DEFIne
  • Arithmetic operations
  • Special symbols
  • IF statements
  • Loops
  • Atom selection
  • Selection by atom name
  • Wildcards and ranges
  • Selection by atom property
  • BYREsidue and BYGRp
  • STOREi and RECALLi
  • Do, show and identity statements
  • 3-D vectors and matrices
  • Output files
  • modules
  • Examples
  
  
• Bibliography
• About this document ...