diff --git a/CMakeLists.txt b/CMakeLists.txt
index 009dfee29..ae14e8a37 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -8,7 +8,7 @@ set(VERSION_PATCH "0")
 
 set(CMAKE_BUILD_TYPE "Release")
 
-cmake_minimum_required(VERSION 2.8.11)
+cmake_minimum_required(VERSION 2.8.12)
 
 if(COMMAND cmake_policy)
   cmake_policy(VERSION 2.6)
@@ -77,8 +77,8 @@ if(APPLE)
   find_package(GLUT REQUIRED)
 endif(APPLE)
 
-set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
-set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
+set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
+set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})
 set(SRCS src/)
 
 # Set bundle info
@@ -92,19 +92,17 @@ If(APPLE)
   set(MACOSX_BUNDLE_COPYRIGHT "${AUTHOR}")
 endif(APPLE)
 
-# Set include directories
-include_directories(
-  ${CMAKE_BINARY_DIR}/src
-  ${CMAKE_SOURCE_DIR}/src
-  ${CMAKE_SOURCE_DIR}/src/gui
-  ${Qt5Widgets_INCLUDE_DIRS}
-  ${Qt5OpenGL_INCLUDE_DIRS}
-  ${Qt5Core_INCLUDE_DIRS}
-  ${Qt5Gui_INCLUDE_DIRS}
-  ${FTGL_INCLUDE_DIRS}
-  ${FREETYPE_INCLUDE_DIRS}
-  ${GLEXT_INCLUDES}
-)
+### htese shall go once is confirmed all is kosher
+#include_directories(
+#  ${CMAKE_BINARY_DIR}/src
+#  ${Qt5Widgets_INCLUDE_DIRS}
+#  ${Qt5OpenGL_INCLUDE_DIRS}
+#  ${Qt5Core_INCLUDE_DIRS}
+#  ${Qt5Gui_INCLUDE_DIRS}
+#  ${FTGL_INCLUDE_DIRS}
+#  ${FREETYPE_INCLUDE_DIRS}
+#  ${GLEXT_INCLUDES}
+#)
 
 # Process CMakeLists in subdirs
 add_subdirectory(${SRCS})
@@ -113,9 +111,13 @@ add_executable(${target_name}
   MACOSX_BUNDLE
   ${SRCS}/main.cpp 
 )
-
+target_include_directories(${target_name} PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+	${PROJECT_BINARY_DIR}/src
+	${PROJECT_SOURCE_DIR}/src/gui
+)
 # Perform final link
-link_directories (${LIBRARY_OUTPUT_PATH})
+#link_directories (${LIBRARY_OUTPUT_PATH})
 IF(WIN32)
   set(ATEN_LINK_LIBS Qt5::Widgets Qt5::Core ${FTGL_LIBRARIES} ${OPENGL_LIBRARIES} ${FREETYPE_LIBRARIES} C:/GnuWin32/lib/libreadline.dll.a)
 ELSEIF(APPLE)
@@ -129,3 +131,15 @@ target_link_libraries( ${target_name}
     ${ATEN_LINK_LIBS}
     )
 
+if(UNIX AND NOT APPLE)
+  INSTALL_TARGET(${target_name} "")
+  configure_file(${PROJECT_SOURCE_DIR}/desktop.cmake Aten.desktop)
+  install(FILES ${PROJECT_SOURCE_DIR}/src/gui/icons/aten.png
+        DESTINATION share/aten)
+  install(FILES ${PROJECT_BINARY_DIR}/Aten.desktop
+        DESTINATION share/applications)
+  foreach(i ff filters fftesting fragments partitions scripts test includes)
+    install(DIRECTORY ${PROJECT_SOURCE_DIR}/data/${i}
+          DESTINATION share/aten)
+  endforeach(i)
+endif(UNIX AND NOT APPLE)
diff --git a/desktop.cmake b/desktop.cmake
index 541d22fd0..74eee170e 100644
--- a/desktop.cmake
+++ b/desktop.cmake
@@ -1,5 +1,5 @@
 [Desktop Entry]
-Version=@VERSION_MAJOR@.@VERSION_MINOR@
+Version=1.0
 Encoding=UTF-8
 Comment=@DESCRIPTION@
 Exec=aten %f
@@ -9,4 +9,5 @@ Name=Aten
 StartupNotify=false
 Terminal=0
 Type=Application
-Categories=Applications
+Categories=Qt;Science;Chemistry;Physics;Math;Education;
+MimeType=chemical/x-cml;chemical/x-xyz;
diff --git a/src/base/CMakeLists.txt b/src/base/CMakeLists.txt
index e1e0848ac..ca5cfffbf 100644
--- a/src/base/CMakeLists.txt
+++ b/src/base/CMakeLists.txt
@@ -75,17 +75,20 @@ add_library(base
   zmatrix.h
   zmatrixelement.h
 )
+target_include_directories(base PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+	${PROJECT_BINARY_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
+)
 
 add_library(fourierdata
   fourierdata.cpp
   fourierdata.h
 )
 
-include_directories(
-  ../
-  ${QT_INCLUDE_DIR}
-  ${CMAKE_SOURCE_DIR}
-  ${CMAKE_BINARY_DIR}
-  ${CMAKE_BINARY_DIR}/src
-  ${CMAKE_SOURCE_DIR}/src/gui
+target_include_directories(fourierdata PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
 )
diff --git a/src/command/CMakeLists.txt b/src/command/CMakeLists.txt
index cb0670bab..2cc3d43b6 100644
--- a/src/command/CMakeLists.txt
+++ b/src/command/CMakeLists.txt
@@ -39,12 +39,13 @@ trajectory.cpp
 transform.cpp
 view.cpp
 )
-
-include_directories(
-../
-${QT_INCLUDE_DIR}
-${CMAKE_SOURCE_DIR}
-${CMAKE_BINARY_DIR}
-${CMAKE_BINARY_DIR}/src
-${CMAKE_SOURCE_DIR}/src/gui
+target_include_directories(command PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+	${PROJECT_BINARY_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
+  ${Qt5Widgets_INCLUDE_DIRS}
+	${PROJECT_SOURCE_DIR}/src/gui
 )
+
+target_link_libraries(command gui) 
diff --git a/src/ff/CMakeLists.txt b/src/ff/CMakeLists.txt
index 06d93ef17..14cd2b818 100644
--- a/src/ff/CMakeLists.txt
+++ b/src/ff/CMakeLists.txt
@@ -18,12 +18,8 @@ add_library(ff
   torsion.cpp 
   vdw.cpp
 )
-
-include_directories(
-../
-${QT_INCLUDE_DIR}
-${CMAKE_BINARY_DIR}
-${CMAKE_SOURCE_DIR}
-${CMAKE_BINARY_DIR}/src
+target_include_directories(ff PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+  ${Qt5Gui_INCLUDE_DIRS}
 )
 
diff --git a/src/gui/CMakeLists.txt b/src/gui/CMakeLists.txt
index db4a4a1f3..20f55f578 100755
--- a/src/gui/CMakeLists.txt
+++ b/src/gui/CMakeLists.txt
@@ -1,15 +1,5 @@
 # Don't forget to include output directory, otherwise
 # the UI file won't be wrapped!
-INCLUDE_DIRECTORIES(
-  ${CMAKE_CURRENT_BINARY_DIR} 
-  ${CMAKE_CURRENT_BINARY_DIR}/../
-  ${Qt5Widgets_INCLUDE_DIRS}
-  ./
-  ../
-  ${CMAKE_SOURCE_DIR}
-  ${CMAKE_BINARY_DIR}
-)
-
 # Meta-Objects
 SET(gui_MOC_HDRS
   command.h
@@ -288,6 +278,11 @@ add_library(gui
   ${gui_SRCS}
   ${gui_MOC_SRCS}
 )
+target_include_directories(gui PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+	${PROJECT_BINARY_DIR}/src
+  ${Qt5Widgets_INCLUDE_DIRS}
+)
 
 # Target 'treegui'
 add_library(treegui
@@ -295,4 +290,9 @@ add_library(treegui
   ${treegui_MOC_SRCS}
   treegui_funcs.cpp
 )
-
+target_include_directories(treegui PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+	${PROJECT_BINARY_DIR}/src
+  ${Qt5Widgets_INCLUDE_DIRS}
+)
+target_link_libraries(treegui gui)
diff --git a/src/main/CMakeLists.txt b/src/main/CMakeLists.txt
index 6aea2e362..7d4b16a0d 100755
--- a/src/main/CMakeLists.txt
+++ b/src/main/CMakeLists.txt
@@ -17,11 +17,12 @@ add_library(main
   probe.cpp
   scripts.cpp
 )
-
-include_directories(
-./
-../
-${QT_INCLUDE_DIR}
-${CMAKE_SOURCE_DIR}/src/gui 
-${CMAKE_BINARY_DIR}
-${CMAKE_BINARY_DIR}/src/)
+target_include_directories(main PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+	${PROJECT_BINARY_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
+  ${Qt5Widgets_INCLUDE_DIRS}
+	${PROJECT_SOURCE_DIR}/src/gui
+)
+target_link_libraries(main gui) 
diff --git a/src/math/CMakeLists.txt b/src/math/CMakeLists.txt
index 9d925995b..4334ed32a 100644
--- a/src/math/CMakeLists.txt
+++ b/src/math/CMakeLists.txt
@@ -9,12 +9,8 @@ add_library(math
   mathfunc.h
   matrix.h
 )
-
-include_directories(
-../
-${QT_INCLUDE_DIR}
-${CMAKE_SOURCE_DIR}
-${CMAKE_BINARY_DIR}
-${CMAKE_BINARY_DIR}/src
-${CMAKE_SOURCE_DIR}/src/gui
+target_include_directories(math PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
 )
diff --git a/src/methods/CMakeLists.txt b/src/methods/CMakeLists.txt
index 91d966bf3..da951d507 100644
--- a/src/methods/CMakeLists.txt
+++ b/src/methods/CMakeLists.txt
@@ -27,11 +27,9 @@ add_library(methods
   rdf.cpp 
   sd.cpp
 )
-
-include_directories(
-../
-${QT_INCLUDE_DIR}
-${CMAKE_BINARY_DIR}
-${CMAKE_SOURCE_DIR}/src/gui
-${CMAKE_BINARY_DIR}/src
+target_include_directories(methods PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
 )
+
diff --git a/src/model/CMakeLists.txt b/src/model/CMakeLists.txt
index df2581cbf..e7dbf8ea4 100644
--- a/src/model/CMakeLists.txt
+++ b/src/model/CMakeLists.txt
@@ -40,11 +40,8 @@ add_library(model
   view.cpp
   zmatrix.cpp
 )
-
-include_directories(
-../
-${QT_INCLUDE_DIR}
-${CMAKE_SOURCE_DIR}
-${CMAKE_BINARY_DIR}
-${CMAKE_BINARY_DIR}/src
+target_include_directories(model PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+  ${Qt5Gui_INCLUDE_DIRS}
 )
+
diff --git a/src/parser/CMakeLists.txt b/src/parser/CMakeLists.txt
index 55b78ad7d..305ddea3d 100644
--- a/src/parser/CMakeLists.txt
+++ b/src/parser/CMakeLists.txt
@@ -110,12 +110,13 @@ widget.cpp
 zmatrix.cpp
 zmatrixelement.cpp
 )
-
-include_directories(
-../
-${QT_INCLUDE_DIR}
-${CMAKE_SOURCE_DIR}
-${CMAKE_BINARY_DIR}
-${CMAKE_BINARY_DIR}/src
-${CMAKE_SOURCE_DIR}/src/gui
+target_include_directories(parser PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+	${PROJECT_BINARY_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
+  ${Qt5Widgets_INCLUDE_DIRS}
+	${PROJECT_SOURCE_DIR}/src/gui
 )
+
+target_link_libraries(parser gui) 
diff --git a/src/render/CMakeLists.txt b/src/render/CMakeLists.txt
index f3ff0dc6a..87bb83e90 100644
--- a/src/render/CMakeLists.txt
+++ b/src/render/CMakeLists.txt
@@ -27,10 +27,10 @@ add_library(render
   textprimitivelist.cpp
 )
 
-include_directories(
-../
-${QT_INCLUDE_DIR}
-${CMAKE_SOURCE_DIR} 
-${CMAKE_BINARY_DIR}
-${CMAKE_BINARY_DIR}/src
+target_include_directories(render PRIVATE
+  ${PROJECT_SOURCE_DIR}/src
+  ${PROJECT_BINARY_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
+  ${FREETYPE_INCLUDE_DIRS}
 )
diff --git a/src/sg/CMakeLists.txt b/src/sg/CMakeLists.txt
index 6f6608ff1..9a38776a0 100644
--- a/src/sg/CMakeLists.txt
+++ b/src/sg/CMakeLists.txt
@@ -10,12 +10,9 @@ add_library(sg
   sgsi.c
   spacegroup.cpp
 )
-
-include_directories(
-  ../
-  ${QT_INCLUDE_DIR}
-  ${CMAKE_SOURCE_DIR}
-  ${CMAKE_BINARY_DIR}
-  ${CMAKE_BINARY_DIR}/src
-  ${CMAKE_SOURCE_DIR}/src/gui
+target_include_directories(sg PRIVATE
+	${PROJECT_SOURCE_DIR}/src
+  ${Qt5Core_INCLUDE_DIRS}
+  ${Qt5Gui_INCLUDE_DIRS}
 )
+