diff --git a/Base.py b/Base.py
index 418b63f..8ffece6 100644
--- a/Base.py
+++ b/Base.py
@@ -28,6 +28,7 @@
     import tkinter.font as tkFont
 
 from subprocess import Popen, PIPE
+from pymol import cmd
 
 import ctypes
 import os
@@ -46,7 +47,7 @@ class Base(object):
     TKINTER_UPDATE_INTERVAL = 100
     
     WEBSITE = 'http://biophys.umontreal.ca/nrg'
-    VERSION = '2.48l'
+    VERSION = '2.48m'
     
     ''' ==================================================================================
     FUNCTION __init__ : Initialization of the variables of the interface
@@ -56,6 +57,7 @@ def __init__(self, root, top, menuindex, Project_Dir, Install_Dir, NRGsuite_Dir,
         self.Name = Name
         self.OSid = OSid
         self.PyMOL = PyMOL
+        self.pymol_major_version = int(cmd.get_version()[0][0])
         
         self.NRGsuite_Dir = NRGsuite_Dir
         self.Install_Dir = Install_Dir
@@ -85,8 +87,8 @@ def __init__(self, root, top, menuindex, Project_Dir, Install_Dir, NRGsuite_Dir,
 
         self.menuindex = menuindex
         if self.menuindex != -1:
-            self.top.menuBar.component('NRGsuite-menu').entryconfig(self.menuindex, state='disabled')
-        
+            self.Disable_MenuItem()
+            
         self.WINDOWWIDTH = WINDOWWIDTH
         self.WINDOWHEIGHT = WINDOWHEIGHT
         
@@ -137,6 +139,36 @@ def __init__(self, root, top, menuindex, Project_Dir, Install_Dir, NRGsuite_Dir,
         
         self.Clean()
                 
+    ''' ==================================================================================
+    FUNCTION Toggle_MenuItem: Toggle the state of the menu item associated to the GUI
+    ==================================================================================  '''  
+    def Toggle_MenuItem(self, state):
+
+        if self.pymol_major_version == 2:
+            k = 0
+            for mi in self.top.menuBar._menudict['NRGsuite'].actions():
+                if k == self.menuindex:
+                    mi.setEnabled(state)
+                    break
+                k += 1
+        else:
+            str_state = 'disabled' if state == False else 'normal'
+            self.top.menuBar.component('NRGsuite-menu').entryconfig(self.menuindex, state=str_state)
+    
+    ''' ==================================================================================
+    FUNCTION Disable_MenuItem: Disable the menu item associated to the GUI
+    ==================================================================================  '''  
+    def Disable_MenuItem(self):
+
+        self.Toggle_MenuItem(False)
+        
+    ''' ==================================================================================
+    FUNCTION Enable_MenuItem: Enable the menu item associated to the GUI
+    ==================================================================================  '''  
+    def Enable_MenuItem(self):
+
+        self.Toggle_MenuItem(True)
+        
     ''' ==================================================================================
     FUNCTION Frame_Main: Generate the Main interface containing ALL the Frames    
     ==================================================================================  '''  
@@ -315,8 +347,8 @@ def Quit(self):
             self.root = None
 
         if self.menuindex != -1:
-            self.top.menuBar.component('NRGsuite-menu').entryconfig(self.menuindex, state='normal')
-                
+            self.Enable_MenuItem()
+
         print('  Closed ' + self.Name)
 
     ''' ==================================================================================
diff --git a/CleftObj.py b/CleftObj.py
index b9487f3..af53d33 100755
--- a/CleftObj.py
+++ b/CleftObj.py
@@ -32,7 +32,7 @@ def __init__(self):
     def Set_CleftMD5(self):
 
         md5 = hashlib.md5()
-        md5.update(self.CleftFile)
+        md5.update(self.CleftFile.encode('utf-8'))
         
         self.CleftMD5 = md5.digest()
     
diff --git a/Color.py b/Color.py
index 540e6ea..02680d9 100755
--- a/Color.py
+++ b/Color.py
@@ -169,4 +169,4 @@ def CreateNoList(pTotColor, pTotalColorList):
     
     noList.sort()
     
-    return noList
+    return [ int(i) for i in noList ]
diff --git a/FlexAID/Config1.py b/FlexAID/Config1.py
index bbf9b43..2cb910d 100755
--- a/FlexAID/Config1.py
+++ b/FlexAID/Config1.py
@@ -915,7 +915,7 @@ def Btn_Import_Clefts(self):
         
 	# LoadFiles can be string instead of list on Windows. here's a workaround
         if self.top.OSid == 'WIN' :
-        	LoadFiles = self.top.root.master.splitlist(LoadFiles) # allows the normalisation of filelists, namely list of lenght 1 under Windows won't be processed as a string anymore
+            LoadFiles = self.top.root.master.splitlist(LoadFiles) # allows the normalisation of filelists, namely list of lenght 1 under Windows won't be processed as a string anymore
 
         if len(LoadFiles) > 0:
 
@@ -930,7 +930,7 @@ def Btn_Import_Clefts(self):
                         Cleft = pickle.load(in_)
                         in_.close()
                         self.Vars.BindingSite.Add_Cleft(Cleft)
-                    
+                        
                     except IOError as IOerr:
                         IOerrMessage = "Could not read the cleft file. Error while loading cleft file : " + LoadFile
                         self.DisplayMessage(IOerrMessage,2)
@@ -1010,7 +1010,7 @@ def Generate_CleftBindingSite(self):
 
         #self.listSpheres = []
 
-        out = file(self.CleftTmpPath, 'w')
+        out = open(self.CleftTmpPath, 'w')
         # print self.Vars.BindingSite.listClefts
         for Cleft in self.Vars.BindingSite.listClefts:
             in_ = open(Cleft.CleftFile, 'r')
diff --git a/FlexAID/IOFile.py b/FlexAID/IOFile.py
index 8edda62..3722181 100755
--- a/FlexAID/IOFile.py
+++ b/FlexAID/IOFile.py
@@ -203,7 +203,7 @@ def Before_Kill_Frame(self):
             
             self.ProcessMolecule( True, self.LigandPath.get(), self.ATOM_INDEX, self.AtomTypes.get(), 
                                   self.Anchor.get(), False, self.ProcessOnly, self.Gen3D.get(), False, 'ligand' )
-            
+
             if self.top.ProcessError:
                 return False
             else:
@@ -994,7 +994,7 @@ def store_InpFile(self):
 
                 #HETTYP  902 1  N1  m   909  910  903    0
                 if Line.startswith('HETTYP'):
-                    
+
                     ATOM = Line[6:11].strip()
 
                     list = []
@@ -1010,10 +1010,10 @@ def store_InpFile(self):
                     INDEX = Line[7:9].strip()
 
                     list = []
-                    for i in range(0,len(Line[10:])/5):
+                    for i in range(0,int(len(Line[10:])/5)):
                         list.append(Line[(10+i*5):(10+5+i*5)].strip())
                     flexInfo[INDEX] = list
-                
+
         except:
             self.DisplayMessage('  ERROR: Could not retrieve ligand input file', 1)
             return 1
diff --git a/FlexAID/ManageFiles.py b/FlexAID/ManageFiles.py
index bfc2951..ac0a218 100755
--- a/FlexAID/ManageFiles.py
+++ b/FlexAID/ManageFiles.py
@@ -218,28 +218,32 @@ def Print_OPTIMZ(self):
     ================================================================================== '''
     def Print_RMSDST(self):
 
+        line = ''
+        
         if self.Config2.UseReference.get():
-            return 'RMSDST ' + self.IOFile.ProcessedLigandPath.get() + '\n'
+            line = 'RMSDST ' + self.IOFile.ProcessedLigandPath.get() + '\n'
         
-        return ''
+        return line
 
     ''' ==================================================================================
     @summary: Print_IMATRX: Prints the IMATRX line of CONFIG input                        
     ================================================================================== '''
     def Print_IMATRX(self):
 
+        line = ''
+        
         if self.IOFile.AtomTypes.get() == 'Sobolev': # 8 atom types only
-            return 'IMATRX ' + os.path.join(self.FlexAID.FlexAIDInstall_Dir,'deps','scr_bin.dat') + '\n'
+            line = 'IMATRX ' + os.path.join(self.FlexAID.FlexAIDInstall_Dir,'deps','scr_bin.dat') + '\n'
 
         elif self.IOFile.AtomTypes.get() == 'Gaudreault': # 12 atom types
-            return 'IMATRX ' + os.path.join(self.FlexAID.FlexAIDInstall_Dir,'deps','M6_cons_3.dat') + '\n'
+            line = 'IMATRX ' + os.path.join(self.FlexAID.FlexAIDInstall_Dir,'deps','M6_cons_3.dat') + '\n'
 
         elif self.IOFile.AtomTypes.get() == 'Sybyl': # 26 atom types
             #return 'IMATRX ' + os.path.join(self.FlexAID.FlexAIDInstall_Dir,'deps','MC_10p_3.dat') + '\n'
             #return 'IMATRX ' + os.path.join(self.FlexAID.FlexAIDInstall_Dir,'deps','MC_5p_norm_P10_M2_2.dat') + '\n'
-            return 'IMATRX ' + os.path.join(self.FlexAID.FlexAIDInstall_Dir,'deps','MC_st0r5.2_6.dat') + '\n'
+            line = 'IMATRX ' + os.path.join(self.FlexAID.FlexAIDInstall_Dir,'deps','MC_st0r5.2_6.dat') + '\n'
             
-        return ''
+        return line
 
     ''' ==================================================================================
     @summary: Print_PERMEA: Prints the PERMEA line of CONFIG input                        
@@ -247,7 +251,8 @@ def Print_IMATRX(self):
     def Print_PERMEA(self):
         
         Permea = 1.00 - float(self.Config3.Permeability.get())
-        return 'PERMEA ' + str(Permea) + '\n'
+        line = 'PERMEA ' + str(Permea) + '\n'
+        return line
 
     ''' ==================================================================================
     @summary: Print_VAR: Prints the VAR* and SPACER lines of CONFIG input
@@ -357,7 +362,7 @@ def Hash_CONFIG(self):
             line += ' %.3f' % self.Config1.Vars.BindingSite.Sphere.Center[2]
             line += ' %.3f\n' % self.Config1.Vars.BindingSite.Sphere.Radius
             
-            hasher.update(line)
+            hasher.update(line.encode('utf-8'))
             
         elif rngOpt == 'LOCCLF':
             self.Config1.Generate_CleftBindingSite()
@@ -372,14 +377,14 @@ def Hash_CONFIG(self):
             
             hasher = General.hashfile_update(self.TmpFile, hasher)
 
-        hasher.update(self.Print_OPTIMZ())
-        hasher.update(self.Print_RMSDST())
-        hasher.update(self.Print_IMATRX())
-        hasher.update(self.Print_PERMEA())
-        hasher.update(self.Print_VAR())
-        hasher.update(self.Print_SLV())
-        hasher.update(self.Print_HET())
-        hasher.update(self.Print_Scoring())
+        hasher.update(self.Print_OPTIMZ().encode('utf-8'))
+        hasher.update(self.Print_RMSDST().encode('utf-8'))
+        hasher.update(self.Print_IMATRX().encode('utf-8'))
+        hasher.update(self.Print_PERMEA().encode('utf-8'))
+        hasher.update(self.Print_VAR().encode('utf-8'))
+        hasher.update(self.Print_SLV().encode('utf-8'))
+        hasher.update(self.Print_HET().encode('utf-8'))
+        hasher.update(self.Print_Scoring().encode('utf-8'))
 
         return hasher.digest()
 
@@ -526,7 +531,7 @@ def Print_FLEXSC(self):
         Permea = 1.00 - float(self.Config3.RotPermeability.get())
         lines += 'ROTPER ' + str(Permea) + '\n'
         
-        return lines
+        return lines.encode('utf-8')
 
     ''' ==================================================================================
     FUNCTION Create_ConsFile: Creates the constraints file
diff --git a/FlexAID/Simulation.py b/FlexAID/Simulation.py
index a086ea8..9a9bcfa 100755
--- a/FlexAID/Simulation.py
+++ b/FlexAID/Simulation.py
@@ -498,8 +498,7 @@ def OrderFledih(self):
             tot = len(self.ListAtom)
             
             # Get all the keys in the Dictionary (ALL the Atoms)
-            order = self.dictFlexBonds.keys()
-            order.sort()
+            order = sorted(list(self.dictFlexBonds.keys()))
         
             for k in order:
         
diff --git a/General.py b/General.py
index c00f695..2598bec 100755
--- a/General.py
+++ b/General.py
@@ -298,7 +298,7 @@ def hashfile_update(file, hasher):
     
     buf = afile.read(BLOCKSIZE)
     while len(buf) > 0:
-        hasher.update(buf)
+        hasher.update(buf.encode('utf-8'))
         buf = afile.read(BLOCKSIZE)
     
     afile.close()
diff --git a/GetCleft/Volume.py b/GetCleft/Volume.py
index ac742c9..890a0cd 100755
--- a/GetCleft/Volume.py
+++ b/GetCleft/Volume.py
@@ -86,6 +86,7 @@ def run(self):
             else:
                 Lines = out.splitlines()
                 for Line in Lines:
+                    Line = Line.decode('utf-8')
                     if Line.startswith('Volume'):
                         Cleft.Volume = float(Line[8:].strip())
                         self.queue.put(lambda: self.top.Init_Table())
diff --git a/Plugin/NRGsuite.py b/Plugin/NRGsuite.py
index 3e04563..b521911 100755
--- a/Plugin/NRGsuite.py
+++ b/Plugin/NRGsuite.py
@@ -40,6 +40,9 @@
 
 import time
 
+from pymol import cmd
+pymol_major_version = int(cmd.get_version()[0][0])
+
 '''=================================================================================================
 FUNCTION get_default_path_for_OSid: returns the default (and preferred) installation path for any OS
 ================================================================================================='''
@@ -123,12 +126,6 @@ def get_default_path_for_OSid():
         #------------------------------------------------------------------# 
         
         def __init__(self):
-            # workaround PyMOL's legacy plugin system
-            if not hasattr(self.menuBar, 'component'):
-                class DummyComponent:
-                    def __init__(self, _): pass
-                    def entryconfig(*_, **_k): pass
-                self.menuBar.component = DummyComponent
             
             self.ProjectName = ''
             self.Project_Dir = ''
@@ -201,9 +198,12 @@ def entryconfig(*_, **_k): pass
                                      'CfgFile',
                                      label='   About',
                                      command = lambda s=self, menuindex=9 : StartAbout(s, menuindex))
-            
+
             # Make the Load  - Create projects button clickable only
-            EnableDisableMenu(self, ['normal','normal','disabled','normal','disabled','disabled','normal'] )
+            if pymol_major_version == 2:
+                EnableDisableMenuQT(self, [True,True,False,True,False,False,True] )
+            else:
+                EnableDisableMenu(self, ['normal','normal','disabled','normal','disabled','disabled','normal'] )
         
         #================================================================================
         # STARTING GetCleft Conditional... 
@@ -277,16 +277,47 @@ def StartCloseProject(self, menuitem):
                     self.RootGetCleft = None
                 print('  GetCleft interface successfully closed.')
                    
-            EnableDisableMenu(self, ['normal','normal','disabled','disabled','disabled','disabled','normal'] )
+            if pymol_major_version == 2:
+                EnableDisableMenuQT(self, [True,True,False,True,False,False,True] )
+            else:
+                EnableDisableMenu(self, ['normal','normal','disabled','normal','disabled','disabled','normal'] )
             
             print('\n  The project \'' + self.ProjectName + '\' was closed.')
 
+        #================================================================================        
+        # Find children item in QMenu
+        #================================================================================
+        def findMenuItem(self, menu, name):
+            for mi in menu.actions():
+                if mi.text().strip() == name:
+                    return mi
+            return None
+
         #================================================================================        
         # Set the NRGsuite Menu Options to Enable when a Project is created or loaded.
         # Set to disable at start up or when a project is closed.
         #================================================================================
-        def EnableDisableMenu(self, states):
+        def EnableDisableMenuQT(self, states):
+
+            menuItems = [
+                'New Project...', 'Load Project...', 'Close Project',
+                'Preferences',
+                'Open FlexAID...', 'Open GetCleft...',
+                'About'
+            ]
+
+            NRGsuite = self.menuBar._menudict['NRGsuite']
+            for menuItem in menuItems:
+                mi = findMenuItem(self, NRGsuite, menuItem)
+                if mi is None: continue
+                mi.setEnabled(states.pop(0))
             
+        #================================================================================        
+        # Set the NRGsuite Menu Options to Enable when a Project is created or loaded.
+        # Set to disable at start up or when a project is closed.
+        #================================================================================
+        def EnableDisableMenu(self, states):
+
             self.menuBar.component('NRGsuite-menu').entryconfig(0, state=states.pop(0))    # new
             self.menuBar.component('NRGsuite-menu').entryconfig(1, state=states.pop(0))    # load
             self.menuBar.component('NRGsuite-menu').entryconfig(2, state=states.pop(0))    # close
diff --git a/Project/LoadProject.py b/Project/LoadProject.py
index d5c81b0..d89c68d 100755
--- a/Project/LoadProject.py
+++ b/Project/LoadProject.py
@@ -328,7 +328,7 @@ def Btn_Cancel_Clicked(self):
     def Btn_Load_Clicked(self, *args):
         
         self.Update_ProjectFile()
-        
+
         self.top.Project_Dir = self.ActualDirPath
         self.top.ProjectName = self.ActualFileName
         
@@ -343,8 +343,11 @@ def Btn_Load_Clicked(self, *args):
     ==================================================================================  '''
     def After_Quit(self):
         
-        NRGsuite.EnableDisableMenu(self.top, [ 'disabled', 'disabled', 'normal', 'normal', 'normal', 'normal', 'normal' ] )
-    
+        if self.pymol_major_version == 2:
+            NRGsuite.EnableDisableMenuQT(self.top, [ False, False, True, True, True, True, True ] )
+        else:
+            NRGsuite.EnableDisableMenu(self.top, [ 'disabled', 'disabled', 'normal', 'normal', 'normal', 'normal', 'normal' ] )            
+
     ''' ==================================================================================
     FUNCTION Btn_Browse_Clicked: Browse to specify the directory to install the project.
     ==================================================================================  '''        
diff --git a/Project/NewProject.py b/Project/NewProject.py
index bab0aba..ba95af4 100755
--- a/Project/NewProject.py
+++ b/Project/NewProject.py
@@ -204,8 +204,11 @@ def Btn_Cancel_Clicked(self):
     FUNCTION After_Quit: Do some tasks after killing a frame
     ==================================================================================  '''
     def After_Quit(self):
-        
-        NRGsuite.EnableDisableMenu(self.top, [ 'disabled', 'disabled', 'normal', 'normal', 'normal', 'normal', 'normal' ] )
+
+        if self.pymol_major_version == 2:
+            NRGsuite.EnableDisableMenuQT(self.top, [ False, False, True, True, True, True, True ] )
+        else:
+            NRGsuite.EnableDisableMenu(self.top, [ 'disabled', 'disabled', 'normal', 'normal', 'normal', 'normal', 'normal' ] )            
 
     ''' ==================================================================================
     FUNCTION Btn_Create_Clicked: Create the new project then quit the application.