ProCKSI

h1. External Software for [[ProCKSI]]

(needs to be updated)

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

<pre>

/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/

</pre>

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

<pre>

/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

</pre>

The following SCOP databases must present:

<pre>

/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

</pre>

h2. Image Software

h3. 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:

<pre>

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

</pre>

On each node copy scripts for automatic x-authentication:

<pre>

cp procksixauth /usr/local/sbin/procksixauth

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

</pre>

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

<pre>

/usr/sbin/gdm-restart

</pre>

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

<pre>

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

</pre>

h3. 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)