diff --git a/modules/base/src/string_ref.hh b/modules/base/src/string_ref.hh
index 802dd594069257ba17213a02d73144018e635b32..38ab290bfa7e97e5aac93b09180dc9b89e0f0af5 100644
--- a/modules/base/src/string_ref.hh
+++ b/modules/base/src/string_ref.hh
@@ -76,7 +76,7 @@ public:
   /// \brief returns a substring of the string
   ///
   /// \param pos the starting position of the substring
-  /// \param length is the length of the string. if std::string::npos, the 
+  /// \param n is the length of the string. if std::string::npos, the
   ///     substring goes from \p pos to the end of the string
   /// The function does on purpose not perform any boundary check in release 
   /// mode. It's the duty of the caller to make sure the string has the required 
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index b02aeab7a02fff665d7217be36db95e438839657..c13dc49f91690a6ec137fb574db0ef02067a4c1f 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -25,9 +25,9 @@ from ost import geom
 
 ## \brief Method to check if naccess executable is present
 #
-# \param naccess Explicit path to msms executable
-# \return         Path to the executable
-# \exception      FileNotFound if executable is not found
+# \param naccess_exe Explicit path to naccess executable
+# \return            Path to the executable
+# \exception         FileNotFound if executable is not found
 def _GetExecutable(naccess_exe):
   return settings.Locate('naccess', explicit_file_name=naccess_exe)
 
@@ -101,11 +101,11 @@ def _ParseAsaFile(entity, file, asa_atom):
       
 ## \brief Reads Area file (.rsa) and attach asa (absolute + relative) per residue to an entitiy
 #
-# \param entity   EntityHandle or EntityView for attaching sasa on atom level
-# \param file     Filename of .rsa file
-# \param asa_atom Name of the float property for absolute SASA
-# \param asa_atom Name of the float property for relative SASA
-# \exception         RuntimeError if residue names are not the same  
+# \param enti       EntityHandle or EntityView for attaching sasa on atom level
+# \param file       Filename of .rsa file
+# \param asa_abs    Name of the float property for absolute SASA
+# \param asa_rel    Name of the float property for relative SASA
+# \exception        RuntimeError if residue names are not the same
 
 def _ParseRsaFile(enti,file, asa_abs, asa_rel):
   area_fh = open(file)
@@ -156,6 +156,7 @@ def __CleanupFiles(dir_name):
 # This method starts the external MSMS executable and returns the stdout of MSMS
 #
 # \param command          Command to execute
+# \param temp_dir
 # \return                 stdout of MSMS
 # \exception              CalledProcessError for non-zero return value
 def _RunNACCESS(command, temp_dir):
@@ -185,7 +186,7 @@ def _RunNACCESS(command, temp_dir):
 # \param include_hetatm     Calculate surface including hetatms
 # \param include_water      Calculate surface including water
 # \param selection          Calculate surface for subset of entity
-# \param naccess  _exe      msms executable (full path to executable)
+# \param naccess_exe        msms executable (full path to executable)
 # \param keep_files         Do not delete temporary files
 # \param asa_abs            Attaches per residue absolute SASA to specified FloatProp on residue level
 # \param asa_rel            Attaches per residue relative SASA to specified FloatProp on residue level
diff --git a/modules/conop/src/nonstandard.hh b/modules/conop/src/nonstandard.hh
index 374694303e1d5d0f05626e7cc43d2f9c53139c5a..a57022def8ef7436889491c7ae6714c6e9a69d6e 100644
--- a/modules/conop/src/nonstandard.hh
+++ b/modules/conop/src/nonstandard.hh
@@ -31,9 +31,6 @@ namespace ost { namespace conop {
 
 
 /// \brief copies all atom of src_res to dst_res, gets compound lib from builder
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the 
-///      dst_residue is not a glycine, it will be inserted if in the dst should
-///      be one and in src it was not present
 
                              
 bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
@@ -41,16 +38,16 @@ bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
                                      ost::mol::XCSEditor& edi);
 
 /// \brief copies all atom of src_res to dst_res, requires a compound lib 
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the 
-///      dst_residue is not a glycine, it will be inserted if in the dst should
-///      be one and in src it was not present
 bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
                                      ost::mol::ResidueHandle dst_res,
                                      ost::mol::XCSEditor& edi, CompoundLibPtr lib);
 
                              
 /// \brief copies all atom of src_res to dst_res
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the 
+/// \param src_res
+/// \param dst_res
+/// \param edi
+/// \param has_cbeta will be set to true if the src_res has a cbeta and the
 ///      dst_residue is not a glycine                             
 bool DLLEXPORT_OST_CONOP CopyIdentical(ost::mol::ResidueHandle src_res,
                                        ost::mol::ResidueHandle dst_res,
diff --git a/modules/gfx/src/entity.hh b/modules/gfx/src/entity.hh
index cddf17d990da1d87b445b177780cde120bacbeb3..9106e260769091b06aac55bc9f346514c73f5e8a 100644
--- a/modules/gfx/src/entity.hh
+++ b/modules/gfx/src/entity.hh
@@ -364,13 +364,13 @@ private:
 
 /// \example load_and_display.py
 /// 
-/// Shows how to  display one \ref Entity "entity" with several render modes
+/// Shows how to  display one \ref ost::gfx::Entity "entity" with several render modes
 /// at once. The sidechains  are displayed simple mode, whereas the backbone is 
 /// displayed with smooth lines.
 
 ///  \example rendermodes.py
 /// 
-/// Shows how to switch between different \ref RenderMode "render modes" and 
+/// Shows how to switch between different \ref ost::gfx::RenderMode "render modes" and
 /// explains some of the rendermode parameters.
 /// \sa \ref load_and_display.py "Loading and Displaying an Entity"
 
@@ -387,7 +387,7 @@ private:
 
 /// \example color_by_property.py
 /// 
-/// Color \ref Entity "graphical entity" by property using a gradient
+/// Color \ref ost::gfx::Entity "graphical entity" by property using a gradient
 /// \sa \ref gradient.py "Gradient Example"
 }} // ns
 
diff --git a/modules/gfx/src/scene.hh b/modules/gfx/src/scene.hh
index 89717de74999e157aeae36443d60333a9e479018..53a935c10f8ff5d21e959f231646d27e8b26c242 100644
--- a/modules/gfx/src/scene.hh
+++ b/modules/gfx/src/scene.hh
@@ -298,7 +298,6 @@ class DLLEXPORT_OST_GFX Scene {
   void Export(const String& fname, unsigned int w,
               unsigned int h, bool transparent=false);
   /// \brief export into bitmap, using multisample anti-aliasing
-  /// \ref Scene::StartOfffscreenMode(unsigned int, unsigned int, int) for more detail
   void Export(const String& fname, unsigned int w,
               unsigned int h, int max_samples, bool transparent=false);
 
@@ -308,7 +307,7 @@ class DLLEXPORT_OST_GFX Scene {
   /// \brief export scene into povray files named fname.pov and fname.inc
   void ExportPov(const std::string& fname, const std::string& wdir=".");
 
-  /// \rbrief export scene via exporter
+  /// \brief export scene via exporter
   void Export(Exporter* ex) const;
 
   //@}
diff --git a/modules/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index ce813e7ef5d1234a8a1686c425629ba9808b7947..227a0db3b969c4cf6f2b8ee91085874cb0b8d9ca 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -22,7 +22,7 @@ import sip
 
 
 ## \brief Opens a DataViewer 
-# \sa \ref fft_li.py "View Fourier Transform Example" \sa \ref modulate_image.py "Modulate Image Example"
+# \sa \example fft_li.py "View Fourier Transform Example" \sa \ref modulate_image.py "Modulate Image Example"
 def _close_event_override_(event):
   print "close event"
 def _set_data_override_(data):
diff --git a/modules/img/alg/src/dft.hh b/modules/img/alg/src/dft.hh
index 9e8d8c6748fd0080dce445fff81db8a6abba8a62..8265dcc102c961595c428ae2b65ebd6a3ab65cb4 100644
--- a/modules/img/alg/src/dft.hh
+++ b/modules/img/alg/src/dft.hh
@@ -30,7 +30,7 @@ namespace ost { namespace img { namespace alg {
 /// \brief Computes Fourier Trasnform honoring the origin of the image
 ///
 ///  \sa \ref view_phase_diff.py "View Phase Diference Example"
-///  \sa \ref code_fragments/img/fft_li.py "View Fourier Transform Example"
+///  \sa \example fft_li.py "View Fourier Transform Example"
 class DLLEXPORT_IMG_ALG DFT: public ConstModOPAlgorithm {
 public:
   DFT();
diff --git a/modules/io/doc/io.dox b/modules/io/doc/io.dox
index 3c864b38b7b8232f1d4314fa2a8529318b3efb9c..b266c977afdc96f07ecd37bdffb06d660e7038f6 100644
--- a/modules/io/doc/io.dox
+++ b/modules/io/doc/io.dox
@@ -28,7 +28,7 @@ control over the exact loading behaviour.
 
 Some of the file formats for molecules do not explicitly define bonds. The
 IO handlers for these file formats make use of the conop module to infer
-connectivity information (see \ref ost::conop::Builder "Builder"). 
+connectivity information.
 
 \subsection io_handler IO Handlers
 
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 58b592b01fe12438b2f4d8e3b5ee603a612ac615..05a46acc3343df263b864e0f5a7a6a4e8245303e 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -210,7 +210,7 @@ except ImportError:
   pass
 
  ## loads several images and puts them in an ImageList
- # \sa \ref code_fragments/img/fft_li.py "View Fourier Transform Example"
+ # \sa \example fft_li.py "View Fourier Transform Example"
 def LoadImageList (files):
   image_list=img.ImageList()
   for file in files:
diff --git a/modules/io/src/mol/star_parser.hh b/modules/io/src/mol/star_parser.hh
index c5febf7fb3c2672c2381cdac72c178e9e93beb9a..53e170e72b6e7f2b0fdfe55b2679c72d10b5ad34 100644
--- a/modules/io/src/mol/star_parser.hh
+++ b/modules/io/src/mol/star_parser.hh
@@ -114,7 +114,7 @@ public:
   /// \brief create a StarParser
   ///
   /// \param stream input stream
-  /// \param item_as_row if true, data-items are first gathered (identifier as
+  /// \param items_as_row if true, data-items are first gathered (identifier as
   ///                    header, values as row) and then parsed like a loop
   ///                    (OnBeginLoop(), OnDataRow(), OnEndLoop())
   explicit StarParser(std::istream& stream, bool items_as_row=false);