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ARIA 1.2 Manual
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ARIA 1.2 Manual
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 ...
Jens Linge 2002-08-01