EBI Groups Thornton Software PoreWalkerLone Operating Manual

PoreWalkerLone Operation

Running PoreWalkerLone

PoreWalkerLone is run from the command line. It runs under linux and assumes you have perl and python both installed as part of your system

To make your life easier, you can set up an alias so that typing porewalker will run the program without you having to enter the full path to the appropriate scripts directory. You can do this by:

alias porewalker [fullpath]/porewalker/scripts/run_porewalker.pl

where [fullpath] points to the location of the PoreWalkerLone programs.

If you use the bash shell, you need to use the command:

export porewalker='[fullpath]/porewalker/scripts/run_porewalker.pl'

The program is run by:

porewalker filename

where filename is the name of the PDB file.

If you have run this file before, the program will warn you that it cannot run because the directory it created previously exists. To force it to overwrite its previous results, run it with a "-r" parameter:

porewalker filename -r

Results

The results of the PoreWalkerLone run are written your PoreWalkerLone results directory - as defined by the RESULTS_DIR parameter in your PARAMS file (see Installation instructions). The results are written to a directory named after your PDB file - with any extension stripped off. So, if your PDB file is called pdb1vjm.ent, the results will be in the directory:

$RESULTS_DIR/pdb1vjm

To view the results, load the index.html file in that directory into your browser.

The results page will look as follows:

Figure 1. Results page for pdb1vjm.ent.

Clicking on the tabs, or on the links in the list, will take you to the various analyses.

Descriptions of the outputs can be found at:

PoreWalker Documentation