diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 57677f7a5df111fefe328e35c1e2e64ba1fcfb4f..30ef45badd45aa1d253fb936b4eff592c21f9408 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -549,13 +549,7 @@ Loading Density Maps
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. function:: LoadImage(filename)
-
-  Load density map from disk with the extension being guessed by the function.
-
-  :param filename: The filename
-  :type  filename: string
-
-.. function:: LoadImage(filename, format)
+              LoadImage(filename, format)
 
   Load density map from disk. If no format is given, the function guesses the 
   filetype based on the extension of the file. If the extension is unknown or not present the
@@ -589,12 +583,8 @@ Loading Density Maps
 Saving Density Maps
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. function:: SaveImage(image,filename)
-
-  Save density map to disk with the function guessing the 
-  filetype based on the file extension.
-
-.. function:: SaveImage(image,filename, format)
+.. function:: SaveImage(image, filename)
+              SaveImage(image, filename, format)
 
   Save density map to disk. If no format is set, the function guesses the 
   filetype based on the file extension.
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index 2be8e65f6aeadc4fb03c7e043ef82f11dde10ab1..24162f9faf5980fcbab03d0b145fce1d0bd5fa6e 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -192,6 +192,7 @@ The basic functionality of editors is implemented in the EditorBase class.
     :returns:         :class:`AtomHandle`
 
   .. method:: InsertAltAtom(residue, atom, alt_group)
+    :noindex:
 
     Insert new atom with alternative position indicator
 
@@ -336,6 +337,7 @@ The basic functionality of editors is implemented in the EditorBase class.
     :type new_numbers: :class:`ResNumList`
 
   .. method:: RenumberChain(chain, start, keep_spacing)
+    :noindex:
 
     Renumber residues of the given chain
               
@@ -409,29 +411,14 @@ Euclidian space.
      atoms positions.
      
      :param transform: The transformation to be applied
-     :type  transform: :class:`geom.Mat4`
-
-  .. method:: ApplyTransform(transform)
-  
-     Apply a transformation to the entity. The transformation is applied to all 
-     atoms positions.
-     
-     :param transform: The transformation to be applied
-     :type  transform: :class:`Transform`
+     :type  transform: :class:`geom.Mat4` or :class:`Transform`
      
   .. method:: SetTransform(transform)
   
      Set the entity transformation. See also :meth:`ApplyTransform`
      
      :param transform: The transformation to be applied
-     :type  transform: :class:`geom.Mat4`
-
-  .. method:: SetTransform(transform)
-  
-     Set the entity transformation. See also :meth:`ApplyTransform`
-     
-     :param transform: The transformation to be applied
-     :type  transform: :class:`Transform`
+     :type  transform: :class:`geom.Mat4` or :class:`Transform`
   
   .. method:: FixTransform()
   
@@ -544,6 +531,7 @@ using an :class:`ICSEditor` is undefined and vice versa.
 
 
   .. method:: SetTorsionAngle(atom1, atom2, atom3, atom4, angle, update_others=True)
+    :noindex:
     
     Set the angles of the given atoms. All connectors at the third atom (A3) will be adjusted accordingly. 
     If you only want to adjust the bond between A3 and A4, and leave 
@@ -587,6 +575,7 @@ using an :class:`ICSEditor` is undefined and vice versa.
 
 
   .. method:: RotateTorsionAngle(atom1, atom2, atom3, atom4, angle, update_others=True)
+    :noindex:
     
     Rotate torsion angle
     
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index f56797a42a3ff28fd856b75bcd18810372317afc..14e3d9fa48d10349b9a5114872e69a4e2edf3a16 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -2343,7 +2343,7 @@ Other Entity-Related Functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. function:: CreateViewFromAtoms(atom_list)
-.. function:: CreateViewFromAtomList(atom_list)
+              CreateViewFromAtomList(atom_list)
 
   Returns a view made up of the atoms in *atom_list*. All atoms are required to
   be atoms of the same entity. Duplicate atoms are only added to the view once.