link to the propka3 command page

docs/source/command.rst

@@ -1,8 +1,10 @@
 .. -*- coding: utf-8 -*-
 
-================================
+.. _propka3-command:
- The :program:`propka3` command
+
-================================
+============================
+ :program:`propka3` command
+============================
 
 PROPKA predicts the pKa values of ionizable groups in proteins and
 protein-ligand complexes based in the 3D structure. The

docs/source/index.rst

@@ -18,8 +18,8 @@ PROPKA 3 predicts the |pKa| values of ionizable groups in proteins
 [Sondergaard2011]_ and protein-ligand complexes based on the 3D
 structure [Olsson2011]_.
 
-This package installs the :program:`propka3` command and the
+This package installs the :ref:`propka3 command <propka3-command>` and
-:mod:`propka` Python package.
+the :mod:`propka` Python package.
 
    
 License and source code

docs/source/quickstart.rst

@@ -8,19 +8,21 @@
  Quickstart Guide
 ==================
 
-PROPKA can be used either as a module or via the installed script :program:`propka3`; i.e., either
+PROPKA can be used either via the installed script :program:`propka3`
+or as a Python module. When using the :ref:`propka3-command`, use
 
 .. code-block:: bash
 
-   propka3
+   propka3  FILENAME
 
-or :mod:`propka`
+As a module (:mod:`propka`), also provide the input filename
 
 .. code-block:: bash
 		
-   python -m propka
+   python -m propka FILENAME
 
-works for invoking PROPKA.
+In both cases, additional options may be added, as described in more
+detail for the :ref:`propka3-command`.
 
 
 Predicting protein residue |pKa| values