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Installation notes (2.2)

This page describes the installation procedure for version 2.2 of ARIA. For version 2.1, see this page.

 

System requirements

ARIA has been extensively tested on different Linux environments (RedHat, Centos, SuSE), and also runs on SGI and Mac OS X. The current version of ARIA supports only CNS as structure calculation engine. However, we plan to support other programs such as CYANA and XPLOR-NIH. Users are welcome to participate to these extensions: If you want to contribute to these efforts, please contact Michael Nilges.

Required software packages

ARIA requires the following third party software packages:

  • CNS 1.1

  • Python 2.3 or later

  • Numeric Python version 21 or later or NumPy 1.0 or later

  • Konrad Hinsen's ScientificPython

  • Tcl/Tk 8.3 or later

  • Tix 8.1.4 or later

  • CCPN Analysis 1.013 or later (Optional)
  • Matplotlib (Optional)

CNS

Academic users can obtain a free license for CNS from the CNS web site at http://cns.csb.yale.edu. Commercial users need to purchase a CNX license from Accelrys (MSI). In order to compile CNS with the ARIA extensions, please do the following:

  • The ARIA fortran sources are located in the subdirectory ./cns/src of the distribution (see section "Installing and running ARIA" below). Please copy all the files to the directory cns_solve_1.1/source of the unpacked cns_solve distribution (this will overwrite some files which is okay).

  • Edit the file "cns_solve_env" in the directory cns_solve_1.1 to define the location of the CNSsolve directory.

  • Go to directory cns_solve_1.1 and type "make install". This should start the compilation process.

Note for Mac OS X:  CNS universal binaries are available from Logan Donaldson' Lab. But the specific aria routines (such as vean statements) are not running on MacIntel.

 

Python

The latest version of Python can be downloaded from the Python homepage at http://www.python.org. Go to the "download" section and download the source tar-ball.The installation is straight forward for most UNIX systems (LINUX in particular). Follow the installation notes of the Python distribution and make sure that Tkinter support is enabled.

Note: In order to install Python with Tcl/Tk support, please make sure that both libraries are installed on your system. If any of the libraries is missing, please check and install the missing components prior to the installtion of Python.

Numeric Python/Numpy

Since maintenance has ceased for Numeric Python, ARIA 2.2 also provides support for the NumPy module.

  • Numeric Python

The Python Numeric extensions (not to be confused with the extensions NumPy) is a popular Python module. It can be obtained from SourceForge at http://sourceforge.net/projects/numpy

. Go to "Download Numerical Python" and download the package "Old Numeric". For installation, please follow instructions provided by the Python Numeric distribution.

 

  • Numpy
The Python Numpy extension is obtainable from SourceForge at http://sourceforge.net/projects/numpy/

. Go to "Download Numerical Python" and download the package "Numpy". Version 1.0 or later is required for ARIA 2.2. For installation, please follow instructions provided by the NumPy distribution.

 

Note: See here for a detail explanation on installing Numeric with ATLAS/LAPACK

 


ScientificPython

Konrad Hinsen's ScientificPython which can be found at http://dirac.cnrs-orleans.fr/plone/software/scientificpython/. Please follow the installation instruction provided by the module.

Note: Using ScientificPython with NumPy requires version 2.7.3 or later of ScientificPython.


CCPN distribution

In order to use the CCPN data model for import/export or data conversion, you also need to install the CCPN data model, and the CCPNMR Analysis software in case you want to export restraint lists, NOE assignments, and analyses of the generated structures, e.g. the result of the violation analysis. The complete CCPN distribution including the API, the FormatConverter, and CCPNMR Analysis can be obtained at http://www.ccpn.ac.uk/ccpn/software.


Matplotlib

Matplotlib is a python 2D plotting library. The mathplotlib library can be found at http://sourceforge.net/projects/matplotlib

.  Download the package "matplotlib" and follow the installation instructions.

 

Note: Matplotlib is not required

for running ARIA 2.2 but necessary for the generation of graphical outputs from ARIA.

Note:

Using Matplotlib with NumPy requires version 0.87.7 or later of Matplotlib.

 

Tcl/Tk and Tix

The Tcl/Tk libraries are obtainable from http://www.tcl.tk. The Tix (Tk Interface eXtension) graphics library provides high-level widgets, extending the standard capabilities of Tk widgets. The latest Tix library can be obtained from SourceForge at http://tix.sourceforge.net. Installing Tix also requires the sources of Tcl/Tk. Make sure that the Tcl/Tk version used during Tix installation matches the version installed on your system (if Python with Tkinter support is already installed, you can check the Tk version linked with Python by using the script "check.py"). Please consult the installation notes for further instructions.

Installing and running ARIA

In order to install ARIA, unpack the ARIA distribution by using the following command:

tar xvzf aria-version_number.tar.gz

This creates the directory tree.

  • You find the source code of ARIA in the directory ./src of the distribution, Python modules are located in ./src/py and /src/py/gui.
  • The CNS protocols implementing, e.g., the simulated annealing protocol used to calculate a structure, are stored in ./cns/protocols. CNS analysis protocols can be found in the sub-directory, ./cns/protocols/analysis.
  • A working example can be found in ./example

Testing the software environment

Python is part of the default installtion of many modern LINUX distributions. If Python is already installed on your system, you can check whether your installation meets all of the requirements for running ARIA by executing the script "check.py" which is located in the root directory of the ARIA distribution:

python <aria-installation-path>/check.py

The script checks the Python version, whether the Numeric package and Tkinter/Tix is installed. Please note, that the script cannot check whether Tcl/Tk/Tix is working properly.

Environment variables

For convenience we suggest adding the following lines to your login script:

csh; edit ".cshrc"

setenv ARIA2 <aria-installation-path>
alias aria2 <Python-executable> -O $ARIA2/aria2.py

bash; edit ".bashrc"

export ARIA2=<aria-installation-path>
alias aria2="<Python-executable> -O $ARIA2/aria2.py" 

zsh; edit ".zshrc"

export ARIA2=<aria-installation-path>
alias aria2="<Python-executable> -O $ARIA2/aria2.py"

Running ARIA

For running the graphical user inferface of ARIA, please use the following command:

aria2 -g

and for help, type

aria2 --help

 

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