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Sourcecode: pymol version File versions

PMGApp.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-*
#-* NOTE: Based on code by John E. Grayson which was in turn 
#-* based on code written by Doug Hellmann. 
#Z* -------------------------------------------------------------------

from Tkinter import *
from tkFileDialog import *

from AbstractApp import AbstractApp
from Setting import Setting
from SetEditor import SetEditor
from ColorEditor import ColorEditor

import Pmw
import sys, string
import pymol
from pymol import cmd
from pymol import util
from pymol import parser

import re
import thread
import threading
import os
from glob import glob
import __builtin__
import traceback
import Queue

def complete(event,str,widget,self):
   st = parser.complete(str.get())
   if st:
      str.set(st)
      widget.icursor(len(st))
   self.focus_entry = 1
   return 1

class PMGApp(AbstractApp):

   appversion     = '0.95'
   appname       = 'PyMOL Tcl/Tk GUI'
   copyright      = 'Copyright (C) 1998-2005 by Warren DeLano and \n DeLano Scientific LLC. All rights reserved.'
   contactweb     = 'http://www.pymol.org'
   contactemail   = 'warren@delanoscientific.com'

   def appInit(self): # create a global variable for the external gui
      pymol._ext_gui = self
      self.fifo = Queue.Queue(0)
      self.save_file = ''

   def execute(self,cmmd): 
      self.fifo.put(cmmd)

   def buttonAdd(self,frame,text,cmd):
      newBtn=Button(frame,
                    text=text,highlightthickness=0,
                    command=cmd,padx=0,pady=0)
      newBtn.pack(side=LEFT,fill=BOTH,expand=YES)

   def get_view(self):
      cmd.get_view(quiet=0)
      try:
         str = cmd.get_view(3,quiet=1)
         self.root.clipboard_clear()
         self.root.clipboard_append(str)
         self.last_view = str
         self.selection_clear()
         self.selection_own()
         self.selection_handle(lambda a,b,s=self:s.last_view)
         print " PyMOL: Viewing matrix copied to clipboard."
      except:
         traceback.print_exc()
      
   def createButtons(self):
      
      row2 = self.createcomponent('row2', (), None,
         Frame,self.get_commandFrame(),bd=0)
      row2.pack(side=TOP,fill=BOTH,expand=YES)
      btn_reset = self.buttonAdd(row2,'Reset',lambda: cmd.do("_ reset"))
      btn_reset = self.buttonAdd(row2,'Zoom',lambda: cmd.do("_ zoom"))      
      btn_rtrace = self.buttonAdd(row2,'Ray',lambda : cmd.do("_ ray"))
      btn_reset = self.buttonAdd(row2,'Rock',lambda :cmd.do("_ rock"))

      row3 = self.createcomponent('row3', (), None,
         Frame,self.get_commandFrame(),bd=0)
      row3.pack(side=TOP,fill=BOTH,expand=YES)
      btn_unpick = self.buttonAdd(row3,'Unpick',lambda : cmd.do("_ unpick"))
      btn_hidesele = self.buttonAdd(row3,'Hide Sele',self.hide_sele)
      btn_getview = self.buttonAdd(row3,'Get View',lambda s=self: s.get_view()) # doesn't get logged

#      row3 = self.createcomponent('row3', (), None,
#         Frame,self.get_commandFrame(),bd=0)
#      row3.pack(side=TOP,fill=BOTH,expand=YES)
#      btn_reset = self.buttonAdd(row3,'Barf',self.quit)
#      btn_reset = self.buttonAdd(row3,'Now',self.quit)
#      btn_reset = self.buttonAdd(row3,'Eat',self.quit)
#      btn_reset = self.buttonAdd(row3,'Shrimp',self.quit)

      row1 = self.createcomponent('row1', (), None,
         Frame,self.get_commandFrame(),bd=0)
      row1.pack(side=TOP,fill=BOTH,expand=YES)
      btn_rewind = self.buttonAdd(row1,'|<',lambda : cmd.do("_ rewind"))
      btn_back = self.buttonAdd(row1,'<',lambda : cmd.do("_ backward"))
      btn_stop = self.buttonAdd(row1,'Stop',lambda : cmd.do("_ mstop"))
      btn_play = self.buttonAdd(row1,'Play',lambda : cmd.do("_ mplay"))
      btn_forward = self.buttonAdd(row1,'>',lambda : cmd.do("_ forward"))
      btn_last = self.buttonAdd(row1,'>|',lambda : cmd.do("_ ending"))
      btn_ccache = self.buttonAdd(row1,'MClear',lambda : cmd.do("_ mclear"))

   def my_show(self,win,center=1):
      if sys.platform!='linux2':
         win.show()
      else: # autocenter, deiconify, and run mainloop
         # this is a workaround for a bug in the
         # interaction between Tcl/Tk and common Linux
         # window managers (namely KDE/Gnome) which causes
         # an annoying 1-2 second delay in opening windows!
         if center:
            tw = win.winfo_reqwidth()+100
            th = win.winfo_reqheight()+100
            vw = win.winfo_vrootwidth()
            vh = win.winfo_vrootheight()
            x = max(0,(vw-tw)/2)
            y = max(0,(vh-tw)/2)
            win.geometry(newGeometry="+%d+%d"%(x,y))
         win.deiconify()
#         win.show()
         
   def my_withdraw(self,win):
      if sys.platform!='linux2':
         win.withdraw()
      else: # autocenter, deiconify, and run mainloop
         win.destroy()

   def my_activate(self,win,center=1,focus=None):
      if sys.platform!='linux2':
         win.activate()
      else: # autocenter, deiconify, and run mainloop
         # this is a workaround for a bug in the
         # interaction between Tcl/Tk and common Linux
         # window managers (namely KDE/Gnome) which causes
         # an annoying 1-2 second delay in opening windows!
         if center:
            tw = win.winfo_reqwidth()+100
            th = win.winfo_reqheight()+100
            vw = win.winfo_vrootwidth()
            vh = win.winfo_vrootheight()
            x = max(0,(vw-tw)/2)
            y = max(0,(vh-tw)/2)
            win.geometry(newGeometry="+%d+%d"%(x,y))
         win.deiconify()
         if focus!=None:
            focus.focus_set()
         win.mainloop()
         
   def my_deactivate(self,win):
      if sys.platform!='linux2':
         win.deactivate()
      else: # autocenter, deiconify, and run mainloop
         win.destroy()

   def back(self):
      if not self.history_cur:
         self.history[0] = self.command.get()
      self.history_cur = (self.history_cur + 1) & self.history_mask
      self.command.set(self.history[self.history_cur])
      l = len(self.history[self.history_cur])
      self.entry.icursor(l)
   
   def forward(self):
      if not self.history_cur:
         self.history[0] = self.command.get()
      self.history_cur = (self.history_cur - 1) & self.history_mask
      self.command.set(self.history[self.history_cur])
      l = len(self.history[self.history_cur])
      self.entry.icursor(l)
      
   def do(self,cmmd):
      self.history[0]=cmmd
      self.history.insert(0,'') # always leave blank at 0
      self.history.pop(self.history_mask+1)
      self.history_cur = 0
      cmd.do(cmmd)
                    
   def createMain(self):
      self.command = StringVar()
      self.entry = self.createcomponent('entry', (), None,
                           Entry,
                           (self.get_dataArea(),),
                           justify=LEFT,
                           width=50,
                           textvariable=self.command)
      self.entry.pack(side=BOTTOM,expand=NO,fill=X)
      self.entry.bind('<Return>',lambda event,w=self.command,s=self:
         (s.do(w.get()),cmd.dirty(),w.set('')))

      self.entry.bind('<Tab>',lambda event,w=self.command,
                      e=self.entry,s=self:
                      complete(event,w,e,s))


      self.history_mask = 0xFF
      self.history = [''] * (self.history_mask+1)
      self.history_cur = 0
      
      self.entry.bind('<Up>',lambda event,w=self.command,
                      e=self.entry,s=self:s.back())

      self.entry.bind('<Down>',lambda event,w=self.command,
                      e=self.entry,s=self:s.forward())

      self.output = self.createcomponent('output', (), None,
                           Pmw.ScrolledText,
                           (self.get_dataArea(),))

      text = self.output.component('text')
      self.text = text
      self.font = 'lucida console'
      if sys.platform[:5]=='linux':
         self.my_fw_font=(self.font,12)
      elif sys.platform[:3]=='win':
         self.my_fw_font=(self.font,8) # Courier 9
      else:
         self.my_fw_font=(self.font,10)
                                                                               
      text.configure(font = self.my_fw_font)
      text.configure(width=72)
      self.focus_entry=0
      self.output.after(1000,self.flush_commands)
      self.output.after(1000,self.update_feedback)
      self.output.after(1000,self.update_menus)
      self.output.pack(side=BOTTOM,expand=YES,fill=BOTH)
      self.bind(self.entry, 'Command Input Area')
      self.initialdir = os.getcwd()
      self.log_file = "log.pml"


      self.bind_all('<F1>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(1,0,0)"))
      self.bind_all('<F2>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(2,0,0)"))
      self.bind_all('<F3>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(3,0,0)"))
      self.bind_all('<F4>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(4,0,0)"))
      self.bind_all('<F5>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(5,0,0)"))
      self.bind_all('<F6>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(6,0,0)"))
      self.bind_all('<F7>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(7,0,0)"))
      self.bind_all('<F8>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(8,0,0)"))
      self.bind_all('<F9>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(9,0,0)"))
      self.bind_all('<F10>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special_special(10,0,0)"))
      self.bind_all('<F11>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special_special(11,0,0)"))
      self.bind_all('<F12>',lambda event,w=self.command,
                      e=self.entry,s=self:cmd.do("cmd._special(12,0,0)"))

   def flush_commands_once(self):
      # flush the external GUI fifo command queue
      while not self.fifo.empty():
         try:
            cmmd = self.fifo.get(0)
            exec cmmd
         except:
            traceback.print_exc()

   def main(self):
      self.flush_commands_once()
      AbstractApp.main(self)
      
   def flush_commands(self):
      self.flush_commands_once()
      self.output.after(20,self.flush_commands) # 50X a second

   def update_feedback(self):
      if self.focus_entry:
         self.focus_entry=0
         self.entry.focus_set()
      for a in cmd.get_feedback():
         self.output.insert(END,"\n")
         self.output.insert(END,a)
         self.output.see(END)
         self.lineCount = self.lineCount + 1
         if self.lineCount > 10000:
            self.output.delete('0.0','%i.%i' % (self.lineCount-5000,0))
            self.lineCount=5000
         self.entry.focus_set()
      self.output.after(100,self.update_feedback) # 10X a second

   def update_menus(self):
      self.setting.refresh()
      self.output.after(500,self.update_menus) # twice a second
      
   def createInterface(self):
         AbstractApp.createInterface(self)
         self.createButtons()
         self.createMain()
         self.lineCount = 0
         startup_pattern = re.sub(r"[\/\\][^\/\\]*$","/startup/*.py*",__file__)
         # startup_pattern = os.environ['PYMOL_PATH']+"/modules/pmg_tk/startup/*.py*"
         raw_list = glob(startup_pattern)
         unique = {}
         for a in raw_list:
            unique[re.sub(r".*[\/\\]|\.py.*$","",a)] = 1
         for name in unique.keys():
            try:
               if name != "__init__":
                  module_context = string.join(string.split(__name__,'.')[0:-1])
                  mod_name = module_context+".startup."+name
                  __builtin__.__import__(mod_name)
                  mod = sys.modules[mod_name]
                  if hasattr(mod,'__init__'):
                     mod.__init__(self)
            except:
               suppress = 0
               # suppress error reporting when using old versions of Python
               if float(sys.version[0:3])<2.3:
                  if( name in ['apbs_tools' ]):
                     suppress = 1
               if not suppress:
                  print "Exception in plugin '%s' -- Traceback follows..."%name
                  traceback.print_exc()
                  print "Error: unable to initialize plugin '%s'."%name
               
   def quit_app(self):
      cmd.log_close()
      cmd.quit()  # avoid logging this - it is inconvenient...

   def file_open(self):
      ofile = askopenfilename(initialdir = self.initialdir,
                              filetypes=[("All Readable","*.pdb"),
                                         ("All Readable","*.ccp4"),
                                         ("All Readable","*.xplor"),
                                         ("All Readable","*.mol"),
                                         ("All Readable","*.mol2"),
                                         ("All Readable","*.sdf"),
                                         ("All Readable","*.xyz"),                                         
                                         ("All Readable","*.r3d"),
                                         ("All Readable","*.cc1"),
                                         ("All Readable","*.cc2"),                                         
                                         ("All Readable","*.ent"),
                                         ("All Readable","*.dat"),
                                         ("All Readable","*.out"),
                                         ("All Readable","*.mmd"),
                                         ("All Readable","*.mmod"),
                                         ("All Readable","*.pse"),
                                         ("All Readable","*.phi"),
                                         ("All Readable","*.fld"),
                                         ("All Readable","*.o"),
                                         ("All Readable","*.omap"),                                         
                                         ("All Readable","*.brix"),
                                         ("All Readable","*.dx"),
                                         ("All Readable","*.pqr"),
                                         ("PDB File","*.pdb"),
                                         ("All Files","*.*"),
                                         ("All Files","*"),                                         
                                         ("PDB File","*.ent"),
                                         ("PyMOL Session","*.pse"),
                                         ("CCP4 Map","*.ccp4"),                                         
                                         ("XPLOR Map","*.xplor"),
                                         ("MOL2/Multi-MOL2","*.mol2"),
                                         ("Macromodel File","*.dat"),
                                         ("Macromodel File","*.out"),
                                         ("Macromodel File","*.mmd"),
                                         ("Macromodel File","*.mmod"),
                                         ("BRIX/O Map","*.o"),
                                         ("BRIX/O Map","*.omap"),
                                         ("BRIX/O Map","*.brix"),
                                         ("DX Map","*.dx"),                                         
                                         ("AVS (MEAD) Field","*.fld"),                                         
                                         ("MOL File","*.mol"),
                                         ("ChemPy Model","*.pkl"),
                                         ("Raster3D Scene","*.r3d"),
                                         ("SDF File","*.sdf"),
                                         ("ChemDraw3D File","*.cc1"),
                                         ("ChemDraw3D File","*.cc2"),
                                         ("Tinker XYZ File","*.xyz")
                                         ])
      if len(ofile):
         self.initialdir = re.sub(r"[^\/\\]*$","",ofile)         
         cmd.log("load %s\n"%ofile,"cmd.load('%s')\n"%ofile)
         if (string.lower(ofile[-4:])=='.pse') and (ofile!=self.save_file):
            self.save_file = '' # remove ambiguous default 
         cmd.load(ofile)

   def install_plugin(self):
      plugdir = os.path.split(__file__)[:-1]
      path = apply(os.path.join,tuple(list(plugdir)+["startup","check_writable"]))
      ok = 1
      try:
         f=open(path,'wb')
         f.close()
         os.unlink(path)
      except:
         ok = 0
         print "Error: Unable to write to plugin directory (insufficient privileges?)."
      if ok:
         ofile = askopenfilename(initialdir = self.initialdir,
                                 filetypes=[("All Readable","*.py"),
                                            ])
         if len(ofile):
            self.initialdir = re.sub(r"[^\/\\]*$","",ofile)
            plugname = os.path.split(ofile)[-1]
            try:
               f=open(ofile,'rb')
               plugin = f.read()
               f.close()
               path = apply(os.path.join,tuple(list(plugdir)+["startup",plugname]))
               f=open(path,'wb')
               f.write(plugin)
               f.close()
               print " Plugin: '%s' installed.  Please restart PyMOL to begin use."%plugname
            except:
               traceback.print_exc()
               print "Error: Sorry, unable to install plugin '%s'."%plugname

   def log_open(self):
      sfile = asksaveasfilename(initialfile = self.log_file,
                                initialdir = self.initialdir,
                                filetypes=[
                                           ("PyMOL Script","*.pml"),
                                           ("PyMOL Program","*.pym"),
                                           ("Python Program","*.py"),
                                           ("All Files","*.*"),
                                           ("All Files","*"),
                                           ])
      if len(sfile):
         self.initialdir = re.sub(r"[^\/\\]*$","",sfile)
         self.log_file = re.sub(r"^.*[^\/\\]","",sfile)
         cmd.log_open(sfile)

   def log_resume(self,append_only=0):
      ofile = askopenfilename(initialdir = os.getcwd(),
                   filetypes=[("All Resumable","*.pml"),
                              ("All Resumable","*.pym"),
                              ("All Resumable","*.py"),
                              ("PyMOL Script","*.pml"),
                              ("PyMOL Program","*.pym"),
                              ("Python Program","*.py"),
                              ("All Files","*.*"),                                           
                              ("All Files","*"),
                              ])
      if len(ofile):
         self.initialdir = re.sub(r"[^\/\\]*$","",ofile)
         self.log_file = re.sub(r"^.*[^\/\\]","",ofile)
         os.chdir(self.initialdir)           
         cmd.resume(ofile)

   def log_append(self,append_only=0):
      ofile = askopenfilename(initialdir = os.getcwd(),
                   filetypes=[("All Appendable","*.pml"),
                              ("All Appendable","*.pym"),
                              ("All Appendable","*.py"),
                              ("PyMOL Script","*.pml"),
                              ("PyMOL Program","*.pym"),
                              ("Python Program","*.py"),
                              ("All Files","*.*"),                                           
                              ("All Files","*"),
                              ])
      if len(ofile):
         self.initialdir = re.sub(r"[^\/\\]*$","",ofile)
         self.log_file = re.sub(r"^.*[^\/\\]","",ofile)
         os.chdir(self.initialdir)           
         cmd.log_open(ofile,'a')

   def session_save(self):
      if self.save_file!='':
         cmd.log("save %s,format=pse\n"%(self.save_file),
                 "cmd.save('%s',format='pse')\n"%(self.save_file))
         cmd.save(self.save_file,"","pse")
      else:
         self.session_save_as()

   def session_save_as(self):
      sfile = asksaveasfilename(initialfile = self.save_file,
                                initialdir = self.initialdir,
                                filetypes=[
         ("PyMOL Session File","*.pse"),
         ])
      if len(sfile):
         if re.search(r"\.pse$|\.PSE$",sfile)==None:
            sfile=sfile+".pse"
         self.initialdir = re.sub(r"[^\/\\]*$","",sfile)
         cmd.log("save %s,format=pse\n"%(sfile),
                 "cmd.save('%s',format='pse')\n"%(sfile))
         cmd.save(sfile,"",format='pse')
         self.save_file = sfile
   
   def file_save(self):
      lst = cmd.get_names('all')
      lst = filter(lambda x:x[0]!="_",lst)
      self.dialog = Pmw.SelectionDialog(self.root,title="Save",
                          buttons = ('OK', 'Cancel'),
                                   defaultbutton='OK',
                          scrolledlist_labelpos=N,
                          label_text='Which object or selection would you like to save?',
                          scrolledlist_items = lst,
                          command = self.file_save2)
      if len(lst):
         listbox = self.dialog.component('scrolledlist')      
         listbox.selection_set(0)
      self.my_show(self.dialog)
      
   def file_save2(self,result):
      if result!='OK':
         self.my_withdraw(self.dialog)
         del self.dialog
      else:
         sels = self.dialog.getcurselection()
         if len(sels)!=0:
            sfile = sels[0]+".pdb"
            self.my_withdraw(self.dialog)
            del self.dialog
            if result=='OK':
               sfile = asksaveasfilename(initialfile = sfile,
                                         initialdir = self.initialdir,
                                         filetypes=[
                                                    ("PDB File","*.pdb"),
                                                    ("MOL File","*.mol"),
                                                    ("MMD File","*.mmd"),
                                                    ("PKL File","*.pkl"),
                                                    ])
               if len(sfile):
                  self.initialdir = re.sub(r"[^\/\\]*$","",sfile)
                  cmd.log("save %s,(%s)\n"%(sfile,sels[0]),
                          "cmd.save('%s','(%s)')\n"%(sfile,sels[0]))
                  cmd.save(sfile,"(%s)"%sels[0])

   def hide_sele(self):
      cmd.log("util.hide_sele()\n","util.hide_sele()\n")
      util.hide_sele()
         
   def file_run(self):
      ofile = askopenfilename(initialdir = os.getcwd(),
                   filetypes=[("All Runnable","*.pml"),
                              ("All Runnable","*.pym"),
                              ("All Runnable","*.py"),
                              ("All Runnable","*.pyc"),
                              ("PyMOL Script","*.pml"),
                              ("Python Program","*.py"),
                              ("Python Program","*.pyc"),
                              ("PyMOL Program","*.pym"),
                              ("All Files","*.*"),                                           
                              ("All Files","*"),
                              ])
      if len(ofile):
         dir = re.sub(r"[^\/\\]*$","",ofile)
         os.chdir(dir)  
         if re.search("\.pym*$|\.PYM*$",ofile):
            cmd.do("run "+ofile);      
         else:
            cmd.do("@"+ofile);

   def file_savepng(self):
      sfile = asksaveasfilename(initialdir = self.initialdir,
             filetypes=[("PNG File","*.png")])
      if len(sfile):
         self.initialdir = re.sub(r"[^\/\\]*$","",sfile)
         cmd.log("png %s\n"%sfile,"cmd.png('%s')\n"%sfile)
         cmd.png(sfile)
         
      
   def file_savemovie(self):
      sfile = asksaveasfilename(filetypes=[("Numbered PNG Files","*.png")])
      if len(sfile):
         self.initialdir = re.sub(r"[^\/\\]*$","",sfile)
         cmd.log("mpng %s\n"%sfile,"cmd.mpng('%s')\n"%sfile)         
         cmd.mpng(sfile)

   def about_plugins(self):
      about = Pmw.MessageDialog((self._hull),
                                title = 'About Plugins',
                                message_text =
    'Plugins are external modules which extend PyMOL\'s capabilities.\n\n Available plugins (if any) are shown in the Plugin menu.\n\nIf no plugins are listed, then either none have been installed, \nor those that are installed are not yet functional.')
      about.activate(geometry='centerscreenfirst')      

   def transparency_menu(self,name,label,setting_name):
      
      self.menuBar.addcascademenu('Transparency', name, label, label=label)
      
      self.menuBar.addmenuitem(name,  'command', 'Off',
                               label='Off',
                               command = lambda : cmd.do("_ cmd.set('%s',0.0)"%setting_name))

      self.menuBar.addmenuitem(name,  'command', '20%',
                               label='20%',
                               command = lambda : cmd.do("_ cmd.set('%s',0.2)"%setting_name))

      self.menuBar.addmenuitem(name,  'command', '40%',
                               label='40%',
                               command = lambda : cmd.do("_ cmd.set('%s',0.4)"%setting_name))

      self.menuBar.addmenuitem(name,  'command', '50%',
                               label='50%',
                               command = lambda : cmd.do("_ cmd.set('%s',0.5)"%setting_name))

      self.menuBar.addmenuitem(name,  'command', '60%',
                               label='60%',
                               command = lambda : cmd.do("_ cmd.set('%s',0.6)"%setting_name))

      self.menuBar.addmenuitem(name,  'command', '80%',
                               label='80%',
                               command = lambda : cmd.do("_ cmd.set('%s',0.8)"%setting_name))

      

   def createMenuBar(self):
      self.menuBar.addmenuitem('Help', 'command',
                               'Get information on application', 
                               label='About', command = lambda : cmd.do("_ splash"))

      self.menuBar.addmenuitem('Help', 'separator', '')

      self.menuBar.addmenuitem('Help', 'command', 'Demo',
                               label='Demo',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,cartoon"))

#      self.menuBar.addmenuitem('Help', 'command', 'Release Notes',
#                               label='Release Notes',
#                               command = lambda: cmd.do("_ cmd.show_help('release')"))

#      self.menuBar.addmenuitem('Help', 'separator', '')
      
#      self.menuBar.addmenuitem('Help', 'command', 'Help on Commands',
#                               label='Commands',
#                               command = lambda: cmd.do("_ cmd.show_help('commands')"))

#      self.menuBar.addmenuitem('Help', 'command', 'Help on Launching',
#                               label='Launching',
#                               command = lambda: cmd.do("_ cmd.show_help('launching')"))      

#      self.menuBar.addmenuitem('Help', 'separator', '')

#      self.menuBar.addmenuitem('Help', 'command', 'Help on Selections',
#                               label='Select Command',
#                               command = lambda: cmd.do("_ cmd.show_help('select')"))      

#      self.menuBar.addmenuitem('Help', 'command', 'Help on Selections',
#                               label='Selection Syntax',
#                               command = lambda: cmd.do("_ cmd.show_help('selections')"))      

#      self.menuBar.addmenuitem('Help', 'command', 'Example Selections',
#                               label='Selection Examples',
#                               command = lambda: cmd.do("_ cmd.show_help('examples')"))      

#      self.menuBar.addmenuitem('Help', 'separator', '')
      

#      self.menuBar.addmenuitem('Help', 'command', 'Help on the Mouse',
#                               label='Mouse',
#                               command = lambda: cmd.do("_ cmd.show_help('mouse')"))      

#      self.menuBar.addmenuitem('Help', 'command', 'Help on the Keyboard',
#                               label='Keyboard',
#                               command = lambda: cmd.do("_ cmd.show_help('keyboard')"))      

#      self.menuBar.addmenuitem('Help', 'command', 'Help on Molecular Editing',
#                               label='Molecular Editing',
#                               command = lambda: cmd.do("_ cmd.show_help('editing')"))      

#      self.menuBar.addmenuitem('Help', 'command', 'Help on Molecular Editing',
#                               label='Molecular Editing Keys',
#                               command = lambda: cmd.do("_ cmd.show_help('edit_keys')"))      

#      self.menuBar.addmenuitem('Help', 'command', 'Help on Stereo',
#                               label='Stereo',
#                               command = lambda: cmd.do("_ cmd.show_help('stereo')"))      

#      self.menuBar.addmenuitem('Help', 'separator', '')
      

#      self.menuBar.addmenuitem('Help', 'command', 'Help on the API',
#                               label='API',
#                               command = lambda: cmd.do("_ cmd.show_help('api')"))      

      self.toggleBalloonVar = IntVar()
      self.toggleBalloonVar.set(0)
      self.setting = Setting()

#      self.menuBar.addmenuitem('Help', 'separator', '')
      
#      self.menuBar.addmenuitem('Help', 'checkbutton',
#                         'Toggle balloon help',
#                         label='Balloon help',
#                        variable = self.toggleBalloonVar,
#                        command=self.toggleBalloon)

      self.menuBar.addmenuitem('File', 'command', 'Open structure file.',
                        label=self.pad+'Open...',
                        command=self.file_open)


      self.menuBar.addmenuitem('File', 'command', 'Save session.',
                        label=self.pad+'Save Session',
                        command=self.session_save)

      self.menuBar.addmenuitem('File', 'command', 'Save session.',
                        label=self.pad+'Save Session As...',
                        command=self.session_save_as)

      self.menuBar.addmenuitem('File', 'command', 'Save structure file.',
                        label=self.pad+'Save Molecule...',
                        command=self.file_save)

#      self.menuBar.addmenuitem('File', 'command', 'Open sequential files.',
#                        label=self.pad+'Open Sequence...',
#                        command=self.file_open)

      self.menuBar.addmenuitem('File', 'command', 'Save current image.',
                        label=self.pad+'Save Image...',
                        command=self.file_savepng)

      self.menuBar.addmenuitem('File', 'command', 'Save all frames.',
                        label=self.pad+'Save Movie...',
                        command=self.file_savemovie)

      self.menuBar.addmenuitem('File', 'separator', '')
      
      self.menuBar.addmenuitem('File', 'command', 'Open log file.',
                        label=self.pad+'Log...',
                        command=self.log_open)

      self.menuBar.addmenuitem('File', 'command', 'Resume log file.',
                        label=self.pad+'Resume...',
                        command=self.log_resume)

      self.menuBar.addmenuitem('File', 'command', 'Append log file.',
                        label=self.pad+'Append...',
                        command=self.log_append)

      self.menuBar.addmenuitem('File', 'command', 'Close log file.',
                        label=self.pad+'Close Log',
                        command=cmd.log_close)

      self.menuBar.addmenuitem('File', 'command', 'Run program or script.',
                        label=self.pad+'Run...',
                        command=self.file_run)


      self.menuBar.addmenuitem('File', 'separator', '')

      self.menuBar.addmenuitem('File', 'command', 'Quit PyMOL',
                        label=self.pad+'Quit',
                        command=self.quit)

      self.menuBar.addmenuitem('File', 'command', 'Reinitialize PyMOL',
                        label=self.pad+'Reinitialize',
                        command=cmd.reinitialize)

#      self.menuBar.addmenuitem('File', 'separator', '')
      
#      self.menuBar.addmenuitem('File', 'checkbutton',
#                         'Log Conformations.',
#                         label=self.pad+'Log Conformations',
#                        variable = self.setting.log_conformations,
#                        command = lambda s=self: s.setting.update('log_conformations'))

#      self.menuBar.addmenuitem('File', 'checkbutton',
#                         'Log Box Selections.',
#                         label=self.pad+'Log Box Selections',
#                        variable = self.setting.log_box_selections,
#                        command = lambda s=self: s.setting.update('log_box_selections'))

      self.menuBar.addmenuitem('Edit', 'command',
                         'To Copy: Use Ctrl-C in TclTk GUI',
                         label='To copy text use Ctrl-C in the TclTk GUI',
                               state='disabled',
                        command =  None)

      self.menuBar.addmenuitem('Edit', 'command',
                         'To Paste, Use Ctrl-V in TclTk GUI',
                         label='To paste text use Ctrl-V in the TckTk GUI',
                               state='disabled',                               
                        command =  None)

      self.menuBar.addmenuitem('Edit', 'separator', '')

      self.menuBar.addmenuitem('Edit', 'command', 'Undo Conformation',
                               label='Undo Conformation [Ctrl-Z]',
                               command = lambda: cmd.do("_ undo"))

      self.menuBar.addmenuitem('Edit', 'command', 'Redo Conformation',
                               label='Redo Conformation [Ctrl-A]',
                               command = lambda: cmd.do("_ redo"))

      self.menuBar.addmenu('Build', 'Build',tearoff=TRUE)

      self.menuBar.addcascademenu('Build', 'Fragment', 'Fragment',
                                  label='Fragment',tearoff=TRUE)
      
#      self.menuBar.addmenu('Fragment', 'Fragment')

      self.menuBar.addmenuitem('Fragment', 'command', 'Acetylene',
                               label='Acetylene [Alt-J]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','acetylene',2,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Amide N->C',
                               label='Amide N->C [Alt-1]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','formamide',3,1)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Amide C->N',
                               label='Amide C->N [Alt-2]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','formamide',5,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Bromine',
                               label='Bromine [Ctrl-B]',
                               command = lambda: cmd.do("_ replace Br,1,1"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Carbon',
                               label='Carbon [Ctrl-C]',
                               command = lambda: cmd.do("_ replace C,4,4"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Carbonyl',
                               label='Carbonyl [Alt-0]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','formaldehyde',2,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Chlorine',
                               label='Chlorine [Ctrl-L]',
                               command = lambda: cmd.do("_ replace Cl,1,1"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Cyclobutyl',
                               label='Cyclobutyl [Alt-4]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','cyclobutane',4,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Cyclopentyl',
                               label='Cyclopentyl [Alt-5]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','cyclopentane',5,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Cyclopentadiene',
                               label='Cyclopentadiene [Alt-8]',
                               command = lambda: cmd.do(
           "_ editor.attach_fragment('pk1','cyclopentadiene',5,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Cyclohexyl',
                               label='Cyclohexyl [Alt-6]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','cyclohexane',7,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Cycloheptyl',
                               label='Cycloheptyl [Alt-7]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','cycloheptane',8,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Fluorine',
                               label='Fluorine [Ctrl-F]',
                               command = lambda: cmd.do("_ replace F,1,1"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Iodine',
                               label='Iodine [Ctrl-I]',
                               command = lambda: cmd.do("_ replace I,1,1"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Methane',
                               label='Methane',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','methane',1,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Nitrogen',
                               label='Nitrogen [Ctrl-N]',
                               command = lambda: cmd.do("_ replace N,4,3"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Oxygen',
                               label='Oxygen [Ctrl-O]',
                               command = lambda: cmd.do("_ replace O,4,2"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Phenyl',
                               label='Phenyl [Alt-9]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','benzene',6,0)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Sulfer',
                               label='Sulfer [Ctrl-S]',
                               command = lambda: cmd.do("_ replace S,2,2"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Sulfonyl',
                               label='Sulfonyl [Alt-3]',
                               command = lambda: cmd.do(
         "_ editor.attach_fragment('pk1','sulfone',3,1)"))

      self.menuBar.addmenuitem('Fragment', 'command', 'Phosphorus',
                               label='Phosphorus [Ctrl-P]',
                               command = lambda: cmd.do("_ replace P,4,3"))

#      self.menuBar.addmenu('Residue', 'Residue')

      self.menuBar.addcascademenu('Build', 'Residue', 'Residue',
                                  label='Residue',tearoff=TRUE)

 
      self.menuBar.addmenuitem('Residue', 'command', 'Acetyl',
                               label='Acetyl [Alt-B]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','ace')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Alanine',
                               label='Alanine [Alt-A]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','ala')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Aspartate',
                               label='Aspartate [Alt-D]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','asp')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Asparagine',
                               label='Asparagine [Alt-N]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','asn')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Arginine',
                               label='Arginine [Alt-R]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','arg')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Cysteine',
                               label='Cysteine [Alt-C]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','cys')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Glutamate',
                               label='Glutamate [Alt-E]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','glu')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Glutamine',
                               label='Glutamine [Alt-N]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','gln')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Glycine',
                               label='Glycine [Alt-G]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','gly')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Histidine',
                               label='Histidine [Alt-H]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','his')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Isoleucine',
                               label='Isoleucine [Alt-I]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','ile')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Leucine',
                               label='Leucine [Alt-L]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','leu')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Lysine',
                               label='Lysine [Alt-K]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','lys')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Methionine',
                               label='Methionine [Alt-M]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','met')"))

      self.menuBar.addmenuitem('Residue', 'command', 'N-Methyl',
                               label='N-Methyl [Alt-Z]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','nme')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Phenylalanine',
                               label='Phenylalanine [Alt-F]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','phe')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Proline',
                               label='Proline [Alt-P]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','pro')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Serine',
                               label='Serine [Alt-S]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','ser')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Threonine',
                               label='Threonine [Alt-T]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','thr')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Tryptophan',
                               label='Tryptophan [Alt-W]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','trp')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Tyrosine',
                               label='Tyrosine [Alt-Y]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','tyr')"))

      self.menuBar.addmenuitem('Residue', 'command', 'Valine',
                               label='Valine [Alt-V]',
                               command = lambda: cmd.do(
         "_ editor.attach_amino_acid('pk1','val')"))


      self.menuBar.addmenuitem('Residue', 'separator', '')
      self.menuBar.addmenuitem('Residue', 'command', 'Helix',
                               label='Helix',
                               command = lambda: cmd.do("_ set secondary_structure,1"))

      self.menuBar.addmenuitem('Residue', 'command', 'Antiparallel Beta Sheet',
                               label='Antiparallel Beta Sheet',
                               command = lambda: cmd.do("_ set secondary_structure,2"))

      self.menuBar.addmenuitem('Residue', 'command', 'Parallel Beta Sheet',
                               label='Parallel Beta Sheet',
                               command = lambda: cmd.do("_ set secondary_structure,3"))

      self.menuBar.addmenuitem('Build', 'separator', '')

      self.menuBar.addcascademenu('Build', 'Sculpting', 'Sculpting',
                                  label='Sculpting',tearoff=TRUE)

      self.menuBar.addmenuitem('Sculpting', 'checkbutton',
                         'Auto-Sculpt.',
                         label=self.pad+'Auto-Sculpting',
                        variable = self.setting.auto_sculpt,
                        command = lambda s=self: s.setting.update('auto_sculpt'))

      self.menuBar.addmenuitem('Sculpting', 'checkbutton',
                         'Sculpting.',
                         label=self.pad+'Sculpting',
                        variable = self.setting.sculpting,
                        command = lambda s=self: s.setting.update('sculpting'))

      self.menuBar.addmenuitem('Sculpting', 'separator', '')
      

      self.menuBar.addmenuitem('Sculpting', 'command', 'Activate',
                               label='Activate',
                               command = lambda: cmd.do("_ sculpt_activate all"))

      self.menuBar.addmenuitem('Sculpting', 'command', 'Deactivate',
                               label='Deactivate',
                               command = lambda: cmd.do("_ sculpt_deactivate all"))

      self.menuBar.addmenuitem('Sculpting', 'command', 'Clear Memory',
                               label='Clear Memory',
                               command = lambda: cmd.do("_ sculpt_purge"))

      self.menuBar.addmenuitem('Sculpting', 'separator', '')

      self.menuBar.addmenuitem('Sculpting', 'command', '1 Cycle/Update',
                               label='1 Cycle per Update',
                               command = lambda: cmd.do("_ set sculpting_cycles=1"))

      self.menuBar.addmenuitem('Sculpting', 'command', '3 Cycles/Update',
                               label='3 Cycles per Update',
                               command = lambda: cmd.do("_ set sculpting_cycles=3"))

      self.menuBar.addmenuitem('Sculpting', 'command', '10 Cycles/Update',
                               label='10 Cycles per Update',
                               command = lambda: cmd.do("_ set sculpting_cycles=10"))

      self.menuBar.addmenuitem('Sculpting', 'command', '33 Cycles/Update',
                               label='33 Cycles per Update',
                               command = lambda: cmd.do("_ set sculpting_cycles=33"))

      self.menuBar.addmenuitem('Sculpting', 'command', '100 Cycles/Update',
                               label='100 Cycles per Update',
                               command = lambda: cmd.do("_ set sculpting_cycles=100"))

      self.menuBar.addmenuitem('Sculpting', 'command', '333 Cycles/Update',
                               label='333 Cycles per Update',
                               command = lambda: cmd.do("_ set sculpting_cycles=333"))

      self.menuBar.addmenuitem('Sculpting', 'command', '1000 Cycles/Update',
                               label='1000 Cycles per Update',
                               command = lambda: cmd.do("_ set sculpting_cycles=1000"))

      self.menuBar.addmenuitem('Sculpting', 'separator', '')

#define cSculptBond  0x01
#define cSculptAngl  0x02
#define cSculptPyra  0x04
#define cSculptPlan  0x08
#define cSculptLine  0x10
#define cSculptVDW   0x20
#define cSculptVDW14 0x40
#define cSculptTors  0x80

      self.menuBar.addmenuitem('Sculpting', 'command', 'Bonds Only',
                               label='Bonds Only',
                               command = lambda: cmd.do("_ set sculpt_field_mask=%d"%(
         0x01)))

      self.menuBar.addmenuitem('Sculpting', 'command', 'Bonds & Angles Only',
                               label='Bonds & Angles Only',
                               command = lambda: cmd.do("_ set sculpt_field_mask=%d"%(
         0x01+0x02)))
      
      self.menuBar.addmenuitem('Sculpting', 'command', 'Local Geometry Only',
                               label='Local Geometry Only',
                               command = lambda: cmd.do("_ set sculpt_field_mask=%d"%(
         0x01+0x02+0x04+0x08+0x10)))

      self.menuBar.addmenuitem('Sculpting', 'command', 'All Except VDW',
                               label='All Except VDW',
                               command = lambda: cmd.do("_ set sculpt_field_mask=%d"%(
         0x01+0x02+0x04+0x08+0x10+0x80)))

      self.menuBar.addmenuitem('Sculpting', 'command', 'All Except 1-4 VDW & Torsions',
                               label='All Except 1-4 VDW & Torsions',
                               command = lambda: cmd.do("_ set sculpt_field_mask=%d"%(
         0x01+0x02+0x04+0x08+0x10+0x20)))

      self.menuBar.addmenuitem('Sculpting', 'command', 'All Terms',
                               label='All Terms',
                               command = lambda: cmd.do("_ set sculpt_field_mask=%d"%(
         0xFF)))


      self.menuBar.addmenuitem('Build', 'separator', '')
      
      self.menuBar.addmenuitem('Build', 'command', 'Cycle Bond Valence',
                               label='Cycle Bond Valence [Ctrl-W]',
                               command = lambda: cmd.do("_ cycle_valence"))

      self.menuBar.addmenuitem('Build', 'command', 'Fill Hydrogens',
                               label='Fill Hydrogens on (pk1) [Ctrl-R]',
                               command = lambda: cmd.do("_ h_fill"))

      self.menuBar.addmenuitem('Build', 'command', 'Invert',
                               label='Invert (pk2)-(pk1)-(pk3) [Ctrl-E]',
                               command = lambda: cmd.do("_ invert"))

      self.menuBar.addmenuitem('Build', 'command', 'Form Bond',
                               label='Create Bond (pk1)-(pk2) [Ctrl-T]',
                               command = lambda: cmd.do("_ bond"))


      self.menuBar.addmenuitem('Build', 'separator', '')

      
      self.menuBar.addmenuitem('Build', 'command', 'Remove (pk1)',
                               label='Remove (pk1) [Ctrl-D]',
                               command = lambda: cmd.do("_ remove pk1"))

      self.menuBar.addmenuitem('Build', 'separator', '')
      
      self.menuBar.addmenuitem('Build', 'command', 'Make Positive',
                               label='Make (pk1) Positive [Ctrl-K]',
                               command = lambda: cmd.do("_ alter pk1,formal_charge=1.0"))

      self.menuBar.addmenuitem('Build', 'command', 'Make Negative',
                               label='Make (pk1) Negative [Ctrl-J]',
                               command = lambda: cmd.do("_ alter pk1,formal_charge=-1.0"))

      self.menuBar.addmenuitem('Build', 'command', 'Make Neutral',
                               label='Make (pk1) Neutral [Ctrl-U]',
                               command = lambda: cmd.do("_ alter pk1,formal_charge=-0.0"))


      self.menuBar.addmenu('Movie', 'Movie Control',tearoff=TRUE)

      
      self.menuBar.addcascademenu('Movie', 'Speed', 'Playback Speed',
                                  label=self.pad+'Speed')

      self.menuBar.addmenuitem('Speed', 'command', 'Maximum',
                               label=self.pad+'Maximum',
                               command = lambda: cmd.set("movie_delay","0",log=1))

      self.menuBar.addmenuitem('Speed', 'command', '30 FPS',
                               label=self.pad+'30 FPS',
                               command = lambda: cmd.set("movie_delay","33",log=1))

      self.menuBar.addmenuitem('Speed', 'command', '15 FPS',
                               label=self.pad+'15 FPS',
                               command = lambda: cmd.set("movie_delay","66",log=1))

      self.menuBar.addmenuitem('Speed', 'command', '5 FPS',
                               label=self.pad+'5 FPS',
                               command = lambda: cmd.set("movie_delay","200",log=1))

      self.menuBar.addmenuitem('Speed', 'command', '1 FPS',
                               label=self.pad+'1 FPS',
                               command = lambda: cmd.set("movie_delay","1000",log=1))

      self.menuBar.addmenuitem('Speed', 'command', '0.3 FPS',
                               label=self.pad+'0.3 FPS',
                               command = lambda: cmd.set("movie_delay","3000",log=1))

      self.menuBar.addmenuitem('Movie', 'command', 'Reset Meter',
                               label=self.pad+'Reset Meter',
                               command = lambda: cmd.do("_ meter_reset"))

      self.menuBar.addmenuitem('Movie', 'separator', '')

      self.menuBar.addmenuitem('Movie', 'checkbutton',
                         'Photorealistic images.',
                         label=self.pad+'Render Frames',
                        variable = self.setting.ray_trace_frames,
                        command = lambda s=self: s.setting.update('ray_trace_frames'))

      self.menuBar.addmenuitem('Movie', 'checkbutton',
                         'Save images in memory.',
                         label=self.pad+'Cache Frames',
                        variable = self.setting.cache_frames,
                        command = lambda s=self: s.setting.update('cache_frames'))

      self.menuBar.addmenuitem('Movie', 'command', 'Flush Cache',
                               label=self.pad+'Flush Cache',
                               command = lambda: cmd.mclear())

      self.menuBar.addmenuitem('Movie', 'separator', '')

      self.menuBar.addmenuitem('Movie', 'checkbutton',
                         'Static Singletons Objects',
                         label=self.pad+'Static Singletons',
                        variable = self.setting.static_singletons,
                        command = lambda s=self: s.setting.update('static_singletons'))

      self.menuBar.addmenuitem('Movie', 'checkbutton',
                         'Superimpose all molecular states.',
                         label=self.pad+'Show All States',
                        variable = self.setting.all_states,
                        command = lambda s=self: s.setting.update('all_states'))

      self.menuBar.addmenu('Display', 'Display Control',tearoff=TRUE)

      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Sequence View',
                         label='Sequence View',
                        variable = self.setting.seq_view,
                        command = lambda s=self: s.setting.update('seq_view'))      

      self.menuBar.addcascademenu('Display', 'Sequence', 'Sequence Mode',
                               label='Sequence Mode')

      self.menuBar.addmenuitem('Sequence', 'command', 'Residue Codes',
                               label='Residue Codes',
                               command = lambda: cmd.do("_ set seq_view_format,0"))

      self.menuBar.addmenuitem('Sequence', 'command', 'Residue Names',
                               label='Residues',
                               command = lambda: cmd.do("_ set seq_view_format,1"))

      self.menuBar.addmenuitem('Sequence', 'command', 'Chain Identifiers',
                               label='Chains',
                               command = lambda: cmd.do("_ set seq_view_format,3"))

      self.menuBar.addmenuitem('Sequence', 'command', 'Atom Names',
                               label='Atoms',
                               command = lambda: cmd.do("_ set seq_view_format,2"))

      self.menuBar.addmenuitem('Sequence', 'command', 'States',
                               label='States',
                               command = lambda: cmd.do("_ set seq_view_format,4"))


      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Stereo View',
                         label='Stereo View',
                        variable = self.setting.stereo,
                        command = lambda s=self: cmd.do("_ stereo "+
                                                        ('off','on')[s.setting.stereo.get()]))
      
#      self.menuBar.addmenuitem('Display', 'command', 'Stereo On',
#                               label='Stereo On',
#                              command = lambda: cmd.do("_ stereo on"))

#      self.menuBar.addmenuitem('Display', 'command', 'Stereo Off',
#                               label='Stereo Off',
#                               command = lambda: cmd.do("_ stereo off"))

      self.menuBar.addcascademenu('Display', 'Stereo', 'Stereo Mode',
                               label='Stereo Mode')

      self.menuBar.addmenuitem('Stereo', 'command', 'Cross-Eye Stereo',
                               label='Cross-Eye Stereo',
                               command = lambda: cmd.do("_ stereo crosseye"))

      self.menuBar.addmenuitem('Stereo', 'command', 'Wall-Eye Stereo',
                               label='Wall-Eye Stereo',
                               command = lambda: cmd.do("_ stereo walleye"))

      self.menuBar.addmenuitem('Stereo', 'command', 'Quad-Buffered Stereo',
                               label='Quad-Buffered Stereo',
                               command = lambda: cmd.do("_ stereo quadbuffer"))

      self.menuBar.addmenuitem('Stereo', 'separator', '')


      self.menuBar.addmenuitem('Stereo', 'command', 'Swap Sides',
                               label='Swap Sides',
                               command = lambda: cmd.do("_ stereo swap"))

      self.menuBar.addmenuitem('Display', 'separator', '')
      
      self.menuBar.addcascademenu('Display', 'Zoom', 'Zoom',
                                  label='Zoom')

      self.menuBar.addmenuitem('Zoom', 'command', '4 Angstrom Sphere',
                               label='4 Angstrom Sphere',
                               command = lambda: cmd.do("_ zoom center,4"))

      self.menuBar.addmenuitem('Zoom', 'command', '6 Angstrom Sphere',
                               label='6 Angstrom Sphere',
                               command = lambda: cmd.do("_ zoom center,6"))

      self.menuBar.addmenuitem('Zoom', 'command', '8 Angstrom Sphere',
                               label='8 Angstrom Sphere',
                               command = lambda: cmd.do("_ zoom center,8"))

      self.menuBar.addmenuitem('Zoom', 'command', '12 Angstrom Sphere',
                               label='12 Angstrom Sphere',
                               command = lambda: cmd.do("_ zoom center,12"))

      self.menuBar.addmenuitem('Zoom', 'command', '20 Angstrom Sphere',
                               label='20 Angstrom Sphere',
                               command = lambda: cmd.do("_ zoom center,20"))

      self.menuBar.addmenuitem('Zoom', 'command', 'All',
                               label='All',
                               command = lambda: cmd.do("_ zoom all"))

      self.menuBar.addmenuitem('Zoom', 'command', 'Complete',
                               label='Complete',
                               command = lambda: cmd.do("_ zoom all,complete=1"))

      self.menuBar.addcascademenu('Display', 'Clip', 'Clip',
                                  label='Clip')

      self.menuBar.addmenuitem('Clip', 'command', 'Nothing',
                               label='Nothing',
                               command = lambda: cmd.do("_ clip atoms,5,all"))

      self.menuBar.addmenuitem('Clip', 'command', '8 Angstrom Slab',
                               label='8 Angstrom Slab',
                               command = lambda: cmd.do("_ clip slab,8"))

      self.menuBar.addmenuitem('Clip', 'command', '12 Angstrom Slab',
                               label='12 Angstrom Slab',
                               command = lambda: cmd.do("_ clip slab,10"))

      self.menuBar.addmenuitem('Clip', 'command', '16 Angstrom Slab',
                               label='16 Angstrom Slab',
                               command = lambda: cmd.do("_ clip slab,15"))

      self.menuBar.addmenuitem('Clip', 'command', '20 Angstrom Slab',
                               label='20 Angstrom Slab',
                               command = lambda: cmd.do("_ clip slab,20"))

      self.menuBar.addmenuitem('Clip', 'command', '30 Angstrom Slab',
                               label='30 Angstrom Slab',
                               command = lambda: cmd.do("_ clip slab,30"))


      self.menuBar.addmenuitem('Display', 'separator', '')

      self.menuBar.addcascademenu('Display', 'Background', 'Background',
                                  label='Background')

      self.menuBar.addmenuitem('Background', 'command', 'White Background',
                               label='White',
                               command = lambda : cmd.do("_ cmd.bg_color('white')"))

      self.menuBar.addmenuitem('Background', 'command', 'Light Grey',
                               label='Light Grey',
                               command = lambda : cmd.do("_ cmd.bg_color('grey80')"))

      self.menuBar.addmenuitem('Background', 'command', 'Grey',
                               label='Grey',
                               command = lambda : cmd.do("_ cmd.bg_color('grey50')"))


      self.menuBar.addmenuitem('Background', 'command', 'Black Background',
                               label='Black',
                               command = lambda : cmd.do("_ cmd.bg_color('black')"))

      self.menuBar.addcascademenu('Display', 'Color Space', 'Color Space',
                                  label='Color Space')

      self.menuBar.addmenuitem('Color Space', 'command', 'CMYK (for publications)',
                               label='CMYK (for publications)',
                               command = lambda : cmd.do("_ cmd.space('cmyk')"))

      self.menuBar.addmenuitem('Color Space', 'command', 'PyMOL (for video & web)',
                               label='PyMOL (for video & web)',
                               command = lambda : cmd.do("_ cmd.space('pymol')"))

      self.menuBar.addmenuitem('Color Space', 'command', 'RGB (default)',
                               label='RGB (default)',
                               command = lambda : cmd.do("_ cmd.space('rgb')"))

      self.menuBar.addcascademenu('Display', 'Performance', 'Performance & Quality',
                                  label='Performance & Quality')

      self.menuBar.addmenuitem('Performance', 'command', 'Maximum Performance',
                               label='Maximum Performance',
                               command = lambda : cmd.do("_ util.performance(100)"))

      self.menuBar.addmenuitem('Performance', 'command', 'Reasonable Performance',
                               label='Reasonable Performance',
                               command = lambda : cmd.do("_ util.performance(66)"))
      
      self.menuBar.addmenuitem('Performance', 'command', 'Reasonable Quality',
                               label='Reasonable Quality',
                               command = lambda : cmd.do("_ util.performance(33)"))

      self.menuBar.addmenuitem('Performance', 'command', 'Maximum Quality',
                               label='Maximum Quality',
                               command = lambda : cmd.do("_ util.performance(0)"))

      
      self.menuBar.addmenuitem('Display', 'separator', '')
      
      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Disable perspective.',
                         label=self.pad+'Orthoscopic View',
                        variable = self.setting.ortho,
                        command = lambda s=self: s.setting.update('ortho'))

      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Use Display Lists.',
                         label=self.pad+'Use Display Lists',
                        variable = self.setting.use_display_lists,
                        command = lambda s=self: s.setting.update('use_display_lists'))

      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Show Valences.',
                         label=self.pad+'Show Valences',
                        variable = self.setting.valence,
                        command = lambda s=self: s.setting.update('valence'))


      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Smooth Lines.',
                         label=self.pad+'Smooth Lines',
                        variable = self.setting.line_smooth,
                        command = lambda s=self: s.setting.update('line_smooth'))

      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Depth Cue (Fogging).',
                         label=self.pad+'Depth Cue',
                        variable = self.setting.depth_cue,
                        command = lambda s=self: s.setting.update('depth_cue'))

      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Two Sided Lighting.',
                         label=self.pad+'Two Sided Lighting',
                        variable = self.setting.two_sided_lighting,
                        command = lambda s=self: s.setting.update('two_sided_lighting'))

      self.menuBar.addmenuitem('Display', 'checkbutton',
                         'Specular Reflections.',
                         label=self.pad+'Specular Reflections',
                        variable = self.setting.specular,
                        command = lambda s=self: s.setting.update('specular'))

      self.menuBar.addmenu('Setting', 'Configuration Control',tearoff=TRUE)

      self.menuBar.addmenuitem('Setting', 'command',
                         'Edit PyMOL Settings',
                         label=self.pad+'Edit All...',
                               command = lambda s=self: SetEditor(s))

      self.menuBar.addmenuitem('Setting', 'command',
                         'Edit PyMOL Colors',
                         label=self.pad+'Colors...',
                               command = lambda s=self: ColorEditor(s))

      self.menuBar.addcascademenu('Setting', 'Cartoon', 'Cartoon',
                                  label=self.pad+'Cartoon')

      self.menuBar.addmenuitem('Cartoon', 'checkbutton',
                         'Round Helices',
                         label=self.pad+'Round Helices',
                        variable = self.setting.cartoon_round_helices,
                        command = lambda s=self: s.setting.update('cartoon_round_helices'))

      self.menuBar.addmenuitem('Cartoon', 'checkbutton',
                         'Fancy Helices',
                         label=self.pad+'Fancy Helices',
                        variable = self.setting.cartoon_fancy_helices,
                        command = lambda s=self: s.setting.update('cartoon_fancy_helices'))

      self.menuBar.addmenuitem('Cartoon', 'checkbutton',
                         'Cylindrical Helices',
                         label=self.pad+'Cylindrical Helices',
                        variable = self.setting.cartoon_cylindrical_helices,
                        command = lambda s=self: s.setting.update('cartoon_cylindrical_helices'))

      self.menuBar.addmenuitem('Cartoon', 'checkbutton',
                         'Flat Sheets',
                         label=self.pad+'Flat Sheets',
                        variable = self.setting.cartoon_flat_sheets,
                        command = lambda s=self: s.setting.update('cartoon_flat_sheets'))


      self.menuBar.addmenuitem('Cartoon', 'checkbutton',
                         'Fancy Sheets',
                         label=self.pad+'Fancy Sheets',
                        variable = self.setting.cartoon_fancy_sheets,
                        command = lambda s=self: s.setting.update('cartoon_fancy_sheets'))

      self.menuBar.addmenuitem('Cartoon', 'checkbutton',
                         'Smooth Loops',
                         label=self.pad+'Smooth Loops',
                        variable = self.setting.cartoon_smooth_loops,
                        command = lambda s=self: s.setting.update('cartoon_smooth_loops'))

      self.menuBar.addmenuitem('Cartoon', 'checkbutton',
                         'Discrete Colors',
                         label=self.pad+'Discrete Colors',
                        variable = self.setting.cartoon_discrete_colors,
                        command = lambda s=self: s.setting.update('cartoon_discrete_colors'))

      self.menuBar.addmenuitem('Cartoon', 'checkbutton',
                         'Highlight Color',
                         label=self.pad+'Highlight Color',
                        variable = self.setting.cartoon_highlight_color,
                        command = lambda s=self: s.setting.update('cartoon_highlight_color'))


      self.menuBar.addcascademenu('Setting', 'Transparency', 'Transparency',
                                  label=self.pad+'Transparency')

      self.transparency_menu('CartoonTransparency','Cartoon','cartoon_transparency')
      self.transparency_menu('SurfaceTransparency','Surface','transparency')
      self.transparency_menu('StickTransparency','Stick','stick_transparency')
      self.transparency_menu('SphereTransparency','Sphere','sphere_transparency')      

      self.menuBar.addmenuitem('Transparency', 'separator', '')
      

      self.menuBar.addmenuitem('Transparency', 'command', 'Uni-Layer',
                               label='Uni-Layer',
                               command = lambda : cmd.do(
         "_ cmd.set('transparency_mode',2);cmd.set('backface_cull',1);cmd.set('two_sided_lighting',0)"))

      self.menuBar.addmenuitem('Transparency', 'command', 'Multi-Layer',
                               label='Multi-Layer',
                               command = lambda : cmd.do(
         "_ cmd.set('transparency_mode',1);cmd.set('backface_cull',0);cmd.set('two_sided_lighting',1)"))

      self.menuBar.addmenuitem('Transparency', 'command', 'Fast and Ugly',
                               label='Fast and Ugly',
                               command = lambda : cmd.do(
         "_ cmd.set('transparency_mode',0);cmd.set('backface_cull',1);cmd.set('two_sided_lighting',0)"))

            
      self.menuBar.addcascademenu('Setting', 'Rendering', 'Rendering',
                                  label=self.pad+'Rendering')

      self.menuBar.addmenuitem('Rendering', 'checkbutton',
                         'Smooth raytracing.',
                         label=self.pad+'Antialias',
                        variable = self.setting.antialias,
                        command = lambda s=self: s.setting.update('antialias'))

      self.menuBar.addmenuitem('Rendering', 'separator', '')
      
      self.menuBar.addcascademenu('Rendering', 'Shadows', 'Shadows',
                               label=self.pad+'Shadows')

      self.menuBar.addmenuitem('Shadows', 'command', 'None',
                               label='None',
                               command = lambda : cmd.do("_ util.ray_shadows('none')"))

      self.menuBar.addmenuitem('Shadows', 'command', 'Light',
                               label='Light',
                               command = lambda : cmd.do("_ util.ray_shadows('light')"))

      self.menuBar.addmenuitem('Shadows', 'command', 'Matte',
                               label='Matte',
                               command = lambda : cmd.do("_ util.ray_shadows('matte')"))

      self.menuBar.addmenuitem('Shadows', 'command', 'Medium',
                               label='Medium',
                               command = lambda : cmd.do("_ util.ray_shadows('medium')"))

      self.menuBar.addmenuitem('Shadows', 'command', 'Heavy',
                               label='Heavy',
                               command = lambda : cmd.do("_ util.ray_shadows('heavy')"))

      self.menuBar.addmenuitem('Shadows', 'command', 'Black',
                               label='Black',
                               command = lambda : cmd.do("_ util.ray_shadows('black')"))

      self.menuBar.addcascademenu('Rendering', 'Texture', 'Texture',
                               label=self.pad+'Texture')

      self.menuBar.addmenuitem('Texture', 'command', 'None',
                               label='None',
                               command = lambda : cmd.do("_ cmd.set('ray_texture',0)"))

      self.menuBar.addmenuitem('Texture', 'command', 'Matte 1',
                               label='Matte 1',
                               command = lambda : cmd.do("_ cmd.set('ray_texture',1)"))

      self.menuBar.addmenuitem('Texture', 'command', 'Matte 2',
                               label='Matte 2',
                               command = lambda : cmd.do("_ cmd.set('ray_texture',4)"))

      self.menuBar.addmenuitem('Texture', 'command', 'Swirl 1',
                               label='Swirl 1',
                               command = lambda : cmd.do("_ cmd.set('ray_texture',2)"))

      self.menuBar.addmenuitem('Texture', 'command', 'Swirl 2',
                               label='Swirl 2',
                               command = lambda : cmd.do("_ cmd.set('ray_texture',3)"))

      self.menuBar.addmenuitem('Texture', 'command', 'Fiber',
                               label='Fiber',
                               command = lambda : cmd.do("_ cmd.set('ray_texture',5)"))

      self.menuBar.addcascademenu('Rendering', 'Interior Texture', 'Interior Texture',
                               label=self.pad+'Interior Texture')

      self.menuBar.addmenuitem('Interior Texture', 'command', 'None',
                               label='None',
                               command = lambda : cmd.do("_ cmd.set('ray_interior_texture',0)"))

      self.menuBar.addmenuitem('Interior Texture', 'command', 'Matte 1',
                               label='Matte 1',
                               command = lambda : cmd.do("_ cmd.set('ray_interior_texture',1)"))

      self.menuBar.addmenuitem('Interior Texture', 'command', 'Matte 2',
                               label='Matte 2',
                               command = lambda : cmd.do("_ cmd.set('ray_interior_texture',4)"))

      self.menuBar.addmenuitem('Interior Texture', 'command', 'Swirl 1',
                               label='Swirl 1',
                               command = lambda : cmd.do("_ cmd.set('ray_interior_texture',2)"))

      self.menuBar.addmenuitem('Interior Texture', 'command', 'Swirl 2',
                               label='Swirl 2',
                               command = lambda : cmd.do("_ cmd.set('ray_interior_texture',3)"))

      self.menuBar.addmenuitem('Interior Texture', 'command', 'Fiber',
                               label='Fiber',
                               command = lambda : cmd.do("_ cmd.set('ray_interior_texture',5)"))


      self.menuBar.addcascademenu('Rendering', 'Memory', 'Memory',
                               label=self.pad+'Memory')

      self.menuBar.addmenuitem('Memory', 'command', 'Use Less (slower)',
                               label='Use Less (slower)',
                               command = lambda : cmd.do("_ cmd.set('hash_max',70,quiet=0)"))

      self.menuBar.addmenuitem('Memory', 'command', 'Use Standard Amount',
                               label='Use Standard Amount',
                               command = lambda : cmd.do("_ cmd.set('hash_max',100,quiet=0)"))

      self.menuBar.addmenuitem('Memory', 'command', 'Use More (faster)',
                               label='Use More (faster)',
                               command = lambda : cmd.do("_ cmd.set('hash_max',170,quiet=0)"))

      self.menuBar.addmenuitem('Memory', 'command', 'Use Even More',
                               label='Use Even More',
                               command = lambda : cmd.do("_ cmd.set('hash_max',230,quiet=0)"))

      self.menuBar.addmenuitem('Memory', 'command', 'Use Most',
                               label='Use Most',
                               command = lambda : cmd.do("_ cmd.set('hash_max',300,quiet=0)"))

      self.menuBar.addmenuitem('Rendering', 'separator', '')

      self.menuBar.addmenuitem('Rendering', 'checkbutton',
                         'Cull Backfaces when Rendering',
                         label=self.pad+'Cull Backfaces',
                        variable = self.setting.backface_cull,
                        command = lambda s=self: s.setting.update('backface_cull'))


      self.menuBar.addmenuitem('Rendering', 'checkbutton',
                         'Opaque Interior Colors',
                         label=self.pad+'Opaque Interiors',
                        variable = self.setting.ray_interior_color,
                        command = lambda s=self: s.setting.update('ray_interior_color'))

      self.menuBar.addmenuitem('Setting', 'separator', '')

      self.menuBar.addcascademenu('Setting', 'Output', 'Output Size',
                                  label=self.pad+'Output Size')

      self.menuBar.addmenuitem('Output', 'command', '8',
                               label='8 Point',
                               command = lambda s=self:
                               s.text.configure(font=(s.font,8)))

      self.menuBar.addmenuitem('Output', 'command', '9',
                               label='9 Point',
                               command = lambda s=self:
                               s.text.configure(font=(s.font,9)))

      self.menuBar.addmenuitem('Output', 'command', '10',
                               label='10 Point',
                               command = lambda s=self:
                               s.text.configure(font=(s.font,10)))

      self.menuBar.addmenuitem('Output', 'command', '11',
                               label='11 Point',
                               command = lambda s=self:
                               s.text.configure(font=(s.font,11)))

      self.menuBar.addmenuitem('Output', 'command', '12',
                               label='12 Point',
                               command = lambda s=self:
                               s.text.configure(font=(s.font,12)))


      self.menuBar.addcascademenu('Setting', 'Control', 'Control Size',
                                  label=self.pad+'Control Size')

      self.menuBar.addmenuitem('Control', 'command', '12',
                               label='12',
                               command = lambda :
                               cmd.do("_ set internal_gui_control_size,12,quiet=1"))

      self.menuBar.addmenuitem('Control', 'command', '14',
                               label='14',
                               command = lambda :
                               cmd.do("_ set internal_gui_control_size,14,quiet=1"))

      self.menuBar.addmenuitem('Control', 'command', '16',
                               label='16',
                               command = lambda :
                               cmd.do("_ set internal_gui_control_size,16,quiet=1"))

      self.menuBar.addmenuitem('Control', 'command', '18',
                               label='18 (default)',
                               command = lambda :
                               cmd.do("_ set internal_gui_control_size,18,quiet=1"))

      self.menuBar.addmenuitem('Control', 'command', '20',
                               label='20',
                               command = lambda :
                               cmd.do("_ set internal_gui_control_size,20,quiet=1"))

      self.menuBar.addmenuitem('Control', 'command', '24',
                               label='24',
                               command = lambda :
                               cmd.do("_ set internal_gui_control_size,24,quiet=1"))

      self.menuBar.addmenuitem('Control', 'command', '30',
                               label='30',
                               command = lambda :
                               cmd.do("_ set internal_gui_control_size,30,quiet=1"))

      self.menuBar.addmenuitem('Setting', 'separator', '')
      
      
      self.menuBar.addmenuitem('Setting', 'checkbutton',
                               'Ignore PDB segi.',
                               label=self.pad+'Ignore PDB Segment Identifier',
                               variable = self.setting.ignore_pdb_segi,
                               command = lambda s=self: s.setting.update('ignore_pdb_segi'))

      self.menuBar.addmenuitem('Setting', 'checkbutton',
                         'Auto-Zoom.',
                         label=self.pad+'Auto-Zoom New Objects',
                        variable = self.setting.auto_zoom,
                        command = lambda s=self: s.setting.update('auto_zoom'))

      self.menuBar.addmenuitem('Setting', 'checkbutton',
                         'Auto-Show Selections.',
                         label=self.pad+'Auto-Show New Selections',
                        variable = self.setting.auto_show_selections,
                        command = lambda s=self: s.setting.update('auto_show_selections'))

      self.menuBar.addmenuitem('Setting', 'checkbutton',
                         'Auto-Hide Selections.',
                         label=self.pad+'Auto-Hide Selections',
                        variable = self.setting.auto_hide_selections,
                        command = lambda s=self: s.setting.update('auto_hide_selections'))

      self.menuBar.addmenuitem('Setting', 'checkbutton',
                         'Auto-Remove Hydrogens.',
                         label=self.pad+'Auto-Remove Hydrogens',
                        variable = self.setting.auto_remove_hydrogens,
                        command = lambda s=self: s.setting.update('auto_remove_hydrogens'))

      self.menuBar.addmenuitem('Setting', 'separator', '')


      self.menuBar.addmenuitem('Setting', 'command', 'Show Text Output',
                               label=self.pad+'Show Text',
                               command = lambda: cmd.set("text","1",log=1))

      self.menuBar.addmenuitem('Setting', 'command', 'Hide Text Output',
                               label=self.pad+'Hide Text',
                               command = lambda: cmd.set("text","0",log=1))

      self.menuBar.addmenuitem('Setting', 'checkbutton',
                         'Overlay Text Output on Graphics',
                         label=self.pad+'Overlay Text',
                        variable = self.setting.overlay,
                        command = lambda s=self: s.setting.update('overlay'))

      self.menuBar.addmenu('Scene', 'Scene Storage',tearoff=TRUE)

      self.menuBar.addcascademenu('Scene', 'Store', 'Store',
                                  label=self.pad+'Store')

      self.menuBar.addcascademenu('Scene', 'Clear', 'Clear',
                                  label=self.pad+'Clear')

      self.menuBar.addmenuitem('Scene', 'separator', '')

      
      for x in range(1,13):
         self.menuBar.addmenuitem('Store', 'checkbutton', 'F%d'%x,
                                  label=self.pad+'F%d'%x,
                                  variable = self.setting.F[x],
                                  command = lambda x=x: cmd.do("scene F%d,store"%x))

         self.menuBar.addmenuitem('Clear', 'checkbutton', 'F%d'%x,
                                  label=self.pad+'F%d'%x,
                                  variable = self.setting.F[x],
                                  command = lambda x=x: cmd.do("scene F%d,clear"%x))

         self.menuBar.addmenuitem('Scene', 'checkbutton', 'Recall F%d'%x,
                                  label=self.pad+'Recall F%d'%x,
                                  variable = self.setting.F[x],
                                  command = lambda x=x: cmd.do("scene F%d"%x))

         
      self.menuBar.addmenu('Mouse', 'Mouse Configuration',tearoff=TRUE)

      self.menuBar.addcascademenu('Mouse', 'SelectionMode', 'Selection Mode',
                                  label='Selection Mode')

      self.menuBar.addmenuitem('SelectionMode', 'command', 'Atoms',
                               label='Atoms',
                               command = lambda :
                               cmd.do("_ set mouse_selection_mode,0,quiet=1"))

      self.menuBar.addmenuitem('SelectionMode', 'command', 'Residues',
                               label='Residues',
                               command = lambda :
                               cmd.do("_ set mouse_selection_mode,1,quiet=1"))

      self.menuBar.addmenuitem('SelectionMode', 'command', 'Chains',
                               label='Chains',
                               command = lambda :
                               cmd.do("_ set mouse_selection_mode,2,quiet=1"))

      self.menuBar.addmenuitem('SelectionMode', 'command', 'Segments',
                               label='Segments',
                               command = lambda :
                               cmd.do("_ set mouse_selection_mode,3,quiet=1"))

      self.menuBar.addmenuitem('SelectionMode', 'command', 'Objects',
                               label='Objects',
                               command = lambda :
                               cmd.do("_ set mouse_selection_mode,4,quiet=1"))

      self.menuBar.addmenuitem('SelectionMode', 'separator', '')

      self.menuBar.addmenuitem('SelectionMode', 'command', 'Molecules',
                               label='Molecules',
                               command = lambda :
                               cmd.do("_ set mouse_selection_mode,5,quiet=1"))

      self.menuBar.addmenuitem('SelectionMode', 'separator', '')

      self.menuBar.addmenuitem('SelectionMode', 'command', 'Molecules',
                               label='C-alphas',
                               command = lambda :
                               cmd.do("_ set mouse_selection_mode,6,quiet=1"))

      self.menuBar.addmenuitem('Mouse', 'separator', '')
      self.menuBar.addmenuitem('Mouse', 'command', '3 Button Viewing Mode',
                               label='3 Button Viewing Mode',
                               command = lambda: cmd.mouse('three_button_viewing'))

      self.menuBar.addmenuitem('Mouse', 'command', '3 Button Editing Mode',
                               label='3 Button Editing Mode',
                               command = lambda: cmd.mouse('three_button_editing'))

      self.menuBar.addmenuitem('Mouse', 'command', '2 Button Viewing Mode',
                               label='2 Button Viewing Mode',
                               command = lambda: cmd.mouse('two_button_viewing'))

      self.menuBar.addmenuitem('Mouse', 'command', '2 Button Selecting Mode',
                               label='2 Button Selecting Mode',
                               command = lambda: cmd.mouse('two_button_selecting'))

      self.menuBar.addmenuitem('Mouse', 'command', '2 Button Editing Mode',
                               label='2 Button Editing Mode',
                               command = lambda: cmd.mouse('two_button_editing'))


      self.menuBar.addmenuitem('Mouse', 'separator', '')

      self.menuBar.addmenuitem('Mouse', 'checkbutton',
                         'Virtual Trackball.',
                         label=self.pad+'Virtual Trackball',
                        variable = self.setting.virtual_trackball,
                        command = lambda s=self: s.setting.update('virtual_trackball'))

      self.menuBar.addmenuitem('Mouse', 'checkbutton',
                         'Roving Origin.',
                         label=self.pad+'Roving Origin',
                        variable = self.setting.roving_origin,
                        command = lambda s=self: s.setting.update('roving_origin'))

      self.menuBar.addmenuitem('Mouse', 'checkbutton',
                         'Roving Detail.',
                         label=self.pad+'Roving Detail',
                        variable = self.setting.roving_detail,
                        command = lambda s=self: s.setting.update('roving_detail'))

      self.menuBar.addmenuitem('Mouse', 'separator', '')
      
      self.menuBar.addmenuitem('Mouse', 'command', '3 Button Universal Cycle',
                               label='3 Button Universal Cycle',
                               command = lambda: cmd.config_mouse('three_button'))

      self.menuBar.addmenuitem('Mouse', 'command', '2 Button Viewing Cycle',
                               label='2 Button Viewing Cycle',
                               command = lambda: cmd.config_mouse('two_button'))

      self.menuBar.addmenuitem('Mouse', 'command', 'Setup 2 Button Editing Cycle',
                               label='2 Button Editing Cycle',
                               command = lambda: cmd.config_mouse('two_button_editing'))

      self.menuBar.addmenu('Wizard', 'Task Wizards',tearoff=TRUE)

      self.menuBar.addmenuitem('Wizard', 'command', 'Appearance',
                               label='Appearance',
                               command = lambda: cmd.do("_ wizard appearance"))

      self.menuBar.addmenuitem('Wizard', 'command', 'Density Map Wizard',
                               label='Density',
                               command = lambda: cmd.do("_ wizard density"))

      self.menuBar.addmenuitem('Wizard', 'command', 'Distance',
                               label='Distance',
                               command = lambda: cmd.do("_ wizard distance"))

      self.menuBar.addmenuitem('Wizard', 'command', 'Filter',
                               label='Filter',
                               command = lambda: cmd.do("_ wizard filter"))

      self.menuBar.addmenuitem('Wizard', 'command', 'Mutagenesis',
                               label='Mutagenesis',
                               command = lambda: cmd.do("_ wizard mutagenesis"))

      self.menuBar.addmenuitem('Wizard', 'command', 'Pair Fitting',
                               label='Pair Fitting',
                               command = lambda: cmd.do("_ wizard pair_fit"))

      self.menuBar.addmenuitem('Wizard', 'command', 'Sculpting',
                               label='Sculpting',
                               command = lambda: cmd.do("_ wizard sculpting"))

      self.menuBar.addmenuitem('Wizard', 'separator', '')
      
      self.menuBar.addmenuitem('Wizard', 'command', 'Label',
                               label='Label',
                               command = lambda: cmd.do("_ wizard label"))

      self.menuBar.addmenuitem('Wizard', 'command', 'Charge',
                               label='Charge',
                               command = lambda: cmd.do("_ wizard charge"))

      self.menuBar.addmenuitem('Wizard', 'separator', '')
      
      self.menuBar.addcascademenu('Wizard', 'Demo', 'Demo',
                                  label='Demo',tearoff=TRUE)

      self.menuBar.addmenuitem('Demo', 'command', 'Representations',
                               label='Representations',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,reps"))

      self.menuBar.addmenuitem('Demo', 'command', 'Cartoon Ribbons',
                               label='Cartoon Ribbons',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,cartoon"))

      self.menuBar.addmenuitem('Demo', 'command', 'Roving Detail',
                               label='Roving Detail',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,roving"))
      
      self.menuBar.addmenuitem('Demo', 'command', 'Roving Density',
                               label='Roving Density',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,roving_density"))

      self.menuBar.addmenuitem('Demo', 'command', 'Transparency',
                               label='Transparency',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,trans"))

      self.menuBar.addmenuitem('Demo', 'command', 'Ray Tracing',
                               label='Ray Tracing',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,ray"))

      self.menuBar.addmenuitem('Demo', 'command', 'Sculpting',
                               label='Sculpting',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,sculpt"))

      self.menuBar.addmenuitem('Demo', 'command', 'Scripted Animation',
                               label='Scripted Animation',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,anime"))


      self.menuBar.addmenuitem('Demo', 'command', 'Electrostatics',
                               label='Electrostatics',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,elec"))


      self.menuBar.addmenuitem('Demo', 'command', 'Compiled Graphics Objects',
                               label='Compiled Graphics Objects',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,cgo"))

      self.menuBar.addmenuitem('Demo', 'command', 'MolScript/Raster3D Input',
                               label='Molscript/Raster3D Input',
                               command = lambda: cmd.do(
         "_ replace_wizard demo,raster3d"))

      self.menuBar.addmenuitem('Demo', 'separator', '')
      
      self.menuBar.addmenuitem('Demo', 'command', 'End Demonstration',
                               label='End Demonstration',
                               command = lambda s=self:cmd.do(
         '_ replace_wizard demo,finish'))

      self.menuBar.addmenu('Plugin', 'Plugin',tearoff=TRUE)      

      self.menuBar.addmenuitem('Plugin', 'command', 'About',
                               label='About Plugins',
                               command = lambda s=self: s.about_plugins())

      self.menuBar.addmenuitem('Plugin', 'command', 'Install Plugin',
                               label='Install Plugin...',
                               command = lambda s=self: s.install_plugin())
      
      self.menuBar.addmenuitem('Plugin', 'separator', '')


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