ProCKSI

= External Software for ProCKSI = 

(needs to be updated)

Generate the following directories on each compute node to contain important executables:

{{{

/usr/local/procksi/CE/

/usr/local/procksi/Cluster/

/usr/local/procksi/DaliLite

/usr/local/procksi/FAST/

/usr/local/procksi/MaxCMO-MSVNS/

/usr/local/procksi/MolScript/

/usr/local/procksi/ROCCH/

/usr/local/procksi/TMalign/

/usr/local/procksi/URMS/

/usr/local/procksi/Vorolign/

/usr/local/procksi/SCOP/

}}}

For the following installation of the ProCKSI server components, the following executables must be present:

{{{

/usr/local/procksi/CE/CE

/usr/local/procksi/Cluster/qclust

/usr/local/procksi/DaliLite/DaliLite

/usr/local/procksi/FAST/fast

/usr/local/procksi/MaxCMO-MSVNS/MaxCMO-MSVNS

/usr/local/procksi/MolScript/molscript

/usr/local/procksi/MolScript/molauto

/usr/local/procksi/ROCCH/ROCCH

/usr/local/procksi/TMalign/TMalign

/usr/local/procksi/URMS/urms

/usr/local/procksi/Vorolign/vorolign.jar

}}}

The following SCOP databases must present:

{{{

/usr/local/procksi/SCOP/dir.cla.scop.txt

/usr/local/procksi/SCOP/dir.cla.scop.txt_UniqueMulti

/usr/local/procksi/SCOP/dir.cla.scop.txt_UniqueSkip

}}}

== Image Software ==

=== !MolScript ===

  * Download ''!MolScript'' from the repository. 

  * Make sure that the ''freeglut'' and ''freeglut-devel'' packages are installed.

  * Compile using the Makefile provided for the x32- or x64-architecture.

!MolScript needs an X display in order to generate images (jpg, gif, …). Its possible to use the console X display for the OpenGL bits even if it is not logged in. Therefore, ''procksi'' must be authenticated and allowed to use this X display virtually.

Get and unpack the ProCKSI x-authentication patch from [repos:Externals/Cluster/xauth.tgz].

On each node copy magic cookie file for x-authentication:

{{{

cp :0.Xauth /var/gdm/:0.Xauth

}}}

On each node copy scripts for automatic x-authentication:

{{{

cp procksixauth /usr/local/sbin/procksixauth

cp :0 /etc/gdm/Init/:0

}}}

Restart the X display manager for the changes to take effect:

{{{

/usr/sbin/gdm-restart

}}}

The virtual X display can be used with unix socket '':0'', e.g.:

{{{

molauto protein.pdb | DISPLAY=unix:0.0 molscript -jpeg -out protein.jpeg

}}}

=== Other Visualisation Software ===

 * Install ''!ImageMagick'' from the [source:Externals/Graphics repository] (sources) if not already installed

 * Install ''Raster3D'' from the [source:Externals/Graphics repository] (sources)

 * Install ''!GraphViz'' from the [source:Externals/Graphics repository] (RPM)

 * Install ''pyparsing'' from the [source:Externals/Python repository] (sources)

 * Install ''pydot'' from the [source:Externals/Python repository] (sources)