--- a/filter/ob_filter.xml	Sat Jun 01 20:02:50 2013 +0200
+++ b/filter/ob_filter.xml	Fri Jul 19 16:27:52 2013 +0200
@@ -138,25 +138,30 @@
   <help>
 
 
-**What does this tool do?**
+.. class:: infomark
+
+**What this tool does**
+
+Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. 
+
+-----
 
-  This tool filters a library of compounds provided by the user, based on a set of physico-chemical user-defined parameters. Multiple parameters can be selected for more specific queries.
+.. class:: warningmark
+
+**Hint**
+
+| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file.
+| 
+| For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
+| 
+| Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).
 
 -----
 
 .. class:: infomark
 
-**Tip:** If your input file is in SDF format you can use the 'Compute physico-chemical properties' tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but its bigger than a SMILES file.
-
-**Tip:** for exact matchings please use the target value for both the minimum and maximum parameters (e.g. a selection of EXACTLY 4 rotatable bonds can be performed by selecting 4 minimum and 4 maximum as values for the property).
-
-**Tip:** selecting multiple times the same property with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).
+**Definition of the pre-defined filtering rules**
 
------
-
-.. class:: infomark
-
-**Definition of the pre-defined filtering rules:**
   **# Lipinski's Rule of Five:**
     =&lt; 5 Hydrogen-bond donor groups
 
@@ -195,15 +200,41 @@
 
 .. class:: infomark
 
-**Output:** the output formats included in this implementation are:
+**Input**
 
-    # sdf formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
+| - `SD-Format`_
+| - `SMILES Format`_
 
-    # SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
+.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
 
 -----
 
-**This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5.
+.. class:: infomark
+
+**Output** 
+
+| SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
+| 
+| SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
+
+.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://journal.chemistrycentral.com/content/2/1/5
+
+N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
+
+.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
+
+`Open Babel`_
+
+.. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
   </help>
 </tool>