more updates to docs

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2615 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/doc/install.rst

@@ -130,10 +130,51 @@ Build Options
    
  * If `OPTIMIZE` is set to 1, an optimized version of OpenStructure is built.
 
+Example Configurations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+**Ubuntu 10.04 Lucid/Lynx**
+
+All the dependencies can be installed from the package manager and are thus located in standard locations. cmake will automatically find them without the need to pass any additional parameters. The only exception is -DOPTIMIZE, which will tell cmake to build an optimized (-O3 -DNDEBUG) version of OpenStructure.
+
+.. code-block:: bash
+
+  cmake . -DOPTIMIZE=1
+
+**MacOS X with MacPorts and optimization turned on**
+
+MacPorts installs all the software under /opt/local. Thus we have to tell cmake where to find Boost, Python and Qt.
+
+.. code-block:: bash
+  
+  cmake . -DBOOST_ROOT=/opt/local -DPYTHON_ROOT=/opt/local \
+        -DSYS_ROOT=/opt/local -DQT_QMAKE_EXECUTABLE=/opt/local/bin/qmake \
+        -DOPTIMIZE=1
+
+
 Building the Project
 --------------------------------------------------------------------------------
 
-Type `make`. If you are using a multi-core machine, you can use the `-j` flag to run
-multiple jobs at once.
+Type `make`. If you are using a multi-core machine, you can use the `-j` flag to 
+run multiple jobs at once.
 
 On Windows run 'Build OpenStructure' from the build menu.
+
+
+
+What's next?
+--------------------------------------------------------------------------------
+
+On Linux and MacOS X, you can start dng from the command-line. The binaries are all located in stage/bin:
+
+.. code-block:: bash
+
+  stage/bin/dng
+  
+or, to start the command-line interpreter:
+
+.. code-block:: bash
+
+  stage/bin/ost
+  
+If you repeatedly use OpenStructure, it is recommended to add /path/to/dng/stage/bin to your path.

modules/doc/intro.rst

@@ -35,7 +35,8 @@ The files we will be using in the tutorial are available in the examples folder
 that comes with OpenStructure. Depending on your platform, the examples are 
 located at a different location:
 
- * on *MacOS X* the files are in /Applications/OpenStructure/Examples
+ * on *MacOS X* the files are located inside the application bundle. The file 
+   browser fill automatically point to the examples.
  * on *Linux* and *Windows* PREFIX/share/openstructure/examples, where PREFIX is 
    the path to the directory containing OpenStructure.
 
@@ -45,7 +46,7 @@ Starting DNG
 The graphical user interface of OpenStructure is called DNG (Dino/DeepView Next 
 Generation). To start it, 
 
- * on *MacOS X* double click DNG.app in /Applications/OpenStructure
+ * on *MacOS X* double click DNG.app
  * on *Windows* double click dng.bat inside the PREFIX/bin directory
  * on *Linux* fire up a terminal change into the OpenStructure installation 
    directory and type 'bin/dng'. If you have the binary directory in the PATH, 

modules/mol/base/doc/entity.rst

@@ -743,17 +743,11 @@ The Handle Classes
 The View Classes
 --------------------------------------------------------------------------------
 
-.. class:: ResidueView
-
-  .. attribute:: handle
-
-    The residue handle this view points to. Also available as 
-    :meth:`GetHandle`.
-  
-    :type: :class:`ResidueHandle`
-
 .. class:: EntityView
 
+  An entity view represents a structural subset of an :class:`EntityHandle`. For 
+  an introduction ,see :doc:`../../intro-01`.
+  
   .. attribute:: chains
    
     List of all chains of this entity. The chains are in the same 
@@ -1290,6 +1284,13 @@ The View Classes
 
 .. class:: ResidueView
 
+  .. attribute:: handle
+
+    The residue handle this view points to. Also available as 
+    :meth:`GetHandle`.
+
+    :type: :class:`ResidueHandle`
+
   .. attribute:: name
 
     The residue name is usually a str of 3 characters, e.g. `GLY` for