Changeset 1135

Timestamp:

Apr 20, 2011 12:30:01 PM (10 years ago)

Author:

lake

Message:

 

Location:

branches/sandbox

Files:

• rbimport_cartesian.tcl (modified) (5 diffs)
• rbimport_fixfrag.tcl (added)
• rbimport_zmatrix.tcl (modified) (6 diffs)
• rigid.tcl (modified) (63 diffs)

branches/sandbox/rbimport_cartesian.tcl

@@ -13 +13 @@
      pack [frame $cart.con -bd 2 -relief groove] -side top
      pack [frame $cart.display -bd 2 -relief groove] -side top -expand 1 -fill both
+     pack [frame $cart.save -bd 2 -relief groove] -side bottom
      wm title $cart "Load rigid body information from cartesian coordinate file"
      wm geometry $cart 600x600+10+10
@@ -29 +30 @@
 
      grid [button $cart.con.but -text "Load Coordinates from File" -width 22 -command "RB_cart $cart.display"] -row 2 -column 1
-     grid [button $cart.con.but2 -text "Save Cartesian Coordinates" -width 22 -command "RB_cart_Build"] -row 3 -column 1
-
-     grid [button $cart.con.but3 -text "Quit" -width 22 -command "destroy .cartesian"] -row 4 -column 1
+     grid [button $cart.save.but2 -text "Save Cartesian \n Coordinates" -width 15 -command "RB_cart_Build"] -row 2 -column 1 -padx 5
+     $cart.save.but2 config -state disable
+     grid [button $cart.save.but3 -text "Abort" -width 15 -command "destroy .cartesian"] -row 2 -column 3 -padx 5 -sticky ns
 }
 
@@ -37 +38 @@
      catch {unset array ::tline}
      set ::rb_file_load [tk_getOpenFile -parent .cartesian -filetypes {
-            {"Cratesian input" .cart} {"All files" *}}]
+            {"Cartesian input" .cart} {"All files" *}}]
      if {[string trim $::rb_file_load] == ""} return
      set fh [open $::rb_file_load r]
@@ -56 +57 @@
      }
      RB_cart_Display $location
+     .cartesian.save.but2 config -state normal
 
- }
+}
 
  proc RB_cart_Display {location args} {
@@ -130 +132 @@
 
      set x 1
+
+     catch {array unset ::rb_x $bodytyp,1,*}
+     catch {array unset ::rb_y $bodytyp,1,*}
+     catch {array unset ::rb_z $bodytyp,1,*}
+
+
      for {set coordnum 1} {$coordnum <= $sitenum} {incr coordnum} {
          if {$::rb_dummy_atom($coordnum) != 1} {

branches/sandbox/rbimport_zmatrix.tcl

@@ -1 +1 @@
 
      set ::rb_loader(zmatrix) RB_Zmat_Load
-     set ::rb_descriptor(zmatrix) "Z-Matrix"
+     set ::rb_descriptor(zmatrix) "Cartesian Coordinates generated by Z-Matrix"
 
 proc RB_Zmat_Load {args} {
@@ -11 +11 @@
      pack [frame $zmat.con -bd 2 -relief groove] -side top
      pack [frame $zmat.display -bd 2 -relief groove] -side top -expand 1 -fill both
+     pack [frame $zmat.save -bd 2 -relief groove] -side bottom
      wm title $zmat "Load rigid body information from Z-Matrix"
      wm geometry $zmat 600x600+10+10
@@ -27 +28 @@
 
      grid [button $zmat.con.but -text "Load Z-Matrix" -width 22 -command "RB_Zmat $zmat.display"] -row 2 -column 1
-     grid [button $zmat.con.but2 -text "Convert to Cartesian" -width 22 -command "RB_Zmat_Convert"] -row 3 -column 1
-     grid [button $zmat.con.but3 -text "Quit" -width 22 -command "destroy .zmatrix"] -row 4 -column 1
+     grid [button $zmat.save.but2 -text "Convert to Cartesian \n Coordnates" -width 17 -command "RB_Zmat_Convert"] -row 2 -column 1 -padx 5
+          $zmat.save.but2 config -state disable
+     grid [button $zmat.save.but3 -text "Abort" -width 17 -command "destroy .zmatrix"] -row 2 -column 2 -padx 5 -sticky ns
+
 }
 
@@ -45 +48 @@
      }
      RB_Zmat_Display $location
+     .zmatrix.save.but2 config -state normal
  }
 
@@ -124 +128 @@
 }
 proc RB_Zmat_Convert {args} {
-     set bodytyp [expr [llength [RigidBodyList]] + 1]
+     set bodytyp [RB_New_RBnum]
+     puts "bodytyp = $bodytyp"
+#     set bodytyp [expr [llength [RigidBodyList]] + 1]
      set atomlist ""
      for {set z 1} {$z <= [expr $::rb_linenum - 1]} {incr z} {
@@ -148 +154 @@
      set coordnum 0
 
+     catch {array unset ::rb_x $bodytyp,1,*}
+     catch {array unset ::rb_y $bodytyp,1,*}
+     catch {array unset ::rb_z $bodytyp,1,*}
+
      foreach coord $coordlist {
              incr coordnum

branches/sandbox/rigid.tcl

@@ -1 @@
- #proc RB_Load_RBdata   loads rigid body data
- #proc RB_Load_Mapdata  loads rigid body mapping data
- #proc RB_Control_Panel
- #proc RB_View_Matrix
- #proc RB_Populate
+# Procedure list:
+# RB_Import_Data_Type {args}            determines types of input available for rigid body creation panel.
+# RB_Load_RBdata {args}                 parses variables from ReadRigidBody
+# RB_Load_Mapdata {phase bodnum mapnum} parses variables from ReadRigidBodyMapping
+# RB_Control_Panel {panelnum args}      builds notebook for rigid bodies
+# RB_Create {args}                      builds rigid body create panel
+# RB_Create_Cart {bodnum location args} creates cartesian coordinate frame in nbt window. (nbt = new body type)
+# RB_Create_save {bodnum args}          builds rigid body from nbt window
+# RB_Delete_Body {bodnum location args} panel queries user confirm rigid body deletion
+# RB_Delete_Body_Confirm {bodnum location args} deletes and unmaps rigid body with UnMapRigidBody and DeleteRigidBody
+# RB_Populate {rb_notebook bodnum args} populates notebook pages with rigid body information
+# RB_Map_New {bodnum args}              adds new map for bodnum
+# RB_View_RMS {address args}            prints RMS data from Fit Rigid Body on mapping panel
+# RB_Choose_Atom {bodnum args}          finds possible first atom for rigid body mapping
+# RB_FitBody2Coords {bodnum menu}          fits rigid body to coordinates.
+# RB_PlotStrBody {bodnum menu}             plots rigid body onto structure
+# RB_Write_Map {args}                   writes mapping information with MapRigidBody
+# RB_Atom_List {phase atomnum address bodnum args} returns a list of atoms in rigid body
+# proc RB_ProcessPhase {bodnum args}    activate / deactivate buttons on rigid body mapping panel
+# RB_Unmap {bodnum args}                writes panel for unmapping rigid body
+# RB_unmap_delete {panel bodnum args}   unmaps rigid body
+# RB_Edit_Matrix {bodnum args}          build edit matrix panel
+# RB_Sort_Inc {bodnum dir args}         sort routine for edit matrix panel (dir = inc or dec)
+# RB_String_Reverse {string args}       reverses the order or elements in a string
+# RB_Matrix_Update {bodnum args}        updates the information in the edit matrix panel
+# proc RB_View_Parameters {phase x y args} not used at this time.
+# proc GetImportFormats {}              locates the file formats for rigid body creation panel not used at this time
+# MakeRBPane {}                         called to initialize pane in notebook
+# NewBodyTypeWindow                      build new rigid body save panel
+# RB_Fixfrag_Load {args}                build panel for generating rigid bodies from exp file
+# RB_FixFragSaveCoord {args}            build rigid body from information on rigid bodies from exp panel
+# RB_FixStartAtom {phase gdisplay gcon2 args}
+# RB_Atom_Fixlist {phase gdisplay}
+# RB_Atom_Origin_Set {args}
+# RB_Geom_Save {args}
+# RB_Refine_Con {args}                  sets matrix to set refinement constrols
+# RB_Variable_Clear {}
+# RB_Con_But_Proc {addresses change args}
+# RB_Con_Button {address args}
+# RB_Var_Gen {varcount args}
+# RB_Var_Assign {args}                   assigns variable numbers to refinement parameters
+# RB_Ref_FlagEnable {phasenum bodnum mapnum var val args}
+# RB_Var_Save {args}
+# RB_TLS_Onoff {phasenum main bodnum mapnum}
+# RB_Load_Vars {phasenum bodnum mapnum args}
+# RB_VarSet {varin mulvarlist args}
+# RB_New_RBnum {args}
+# RB_CartesianTextFile {bodnum args}
+
+
+
+# Important Global variable list:
+#          ::rbtypelist                               variable that contains RB file format types.
+#          ::rb_map(bodnum)                           number of times rigid body is mapped.
+#          ::rb_matrix_num(bodnum)                    number of matrices in rigid body.
+#          ::rb_mult(bodnum,matrixnum)                multiplier for matrix.
+#          ::rb_damp(bodnum,matrixnum)                damping factor for matrix multiplier.
+#          ::rb_var(bodnum,matrixnum)                 variable id for matrix multiplier.
+#          ::rb_coord_num(bodnum,matrixnum)           number of coordinates associated with matrix.
+#          ::rb_coord(bodnum,matrixnum,coord)         coordinate list
+#          ::rb_x(bodnum,matrixnum,coordnum)          x coordinate
+#          ::rb_y(bodnum,matrixnum,coordnum)          y coordinate
+#          ::rb_z(bodnum,matrixnum,coordnum)          z coordinate
+#          ::rb_lbl(bodnum,matrixnum,coordnum)        label for coordinate triplet
+#          ::rb_map_beginning(phase,bodnum,mapnum)    first atom in list
+#          ::rb_map_origin(phase,bodnum,mapnum)       origin of rigid body
+#          ::rb_map_euler(phase,bodnum,mapnum)        euler angles of rigid body
+#          ::rb_map_positions(phase,bodnum,mapnum)    positions
+#          ::rb_map_damping(phase,bodnum,mapnum)      damping
+#          ::rb_map_tls(phase,bodnum,mapnum)          tls
+#          ::rb_map_tls_var(phase,bodnum,mapnum)      tls variable id number
+#          ::rb_map_tls_damp(phase,bodnum,mapnum)     tls damping factor
+#          ::rb_notebook                              contains address of rigid body notebook
+#          ::rb_firstatom                             contains first atom on active rigid body.  Must be gobal for variable has trace.
+#$         ::rb_phase                                 phase for active map
 
 # debug code to load test files when run as an independent script
@@ -23 +93 @@
     source [file join $expgui(scriptdir) rb.tcl]
 }
-################################################################
+
 # Procedure to determine possible RB file formats available
 
@@ -42 +112 @@
     return $::rbtypelist
 }
-############################################################
-#global variables generated by RB_Load         (x = rigid body number
-#                                              y = matrix number
-#                                              z = coordinate number
-#          ::rb_map(bodytyp)                   number of times rigid body is mapped.
-#          ::rb_matrix_num(bodytyp)            number of matrices in rigid body.
-#          ::rb_mult(bodytyp,matrixnum)        multiplier for matrix.
-#          ::rb_damp(bodytyp,matrixnum)        damping factor for matrix.
-#          ::rb_var(bodytyp,matrixnum)         variable for matrix.
-#          ::rb_coord_num(bodytyp,matrixnum)   number of coordinates associated with matrix.
-#          ::rb_coord(bodytyp,matrixnum,coord) coordinates
-#          ::rb_x(bodytyp,matrixnum,coordnum)  x coordinate
-#          ::rb_y(bodytyp,matrixnum,coordnum)  y coordinate
-#          ::rb_z(bodytyp,matrixnum,coordnum   z coordinate
-#          ::rb_lbl(bodytyp,matrixnum,coordnum label for coordinate triplet
+
+
+#global variables generated by RB_Load
+#
+#
+#          ::rb_map(bodnum)                   number of times rigid body is mapped.
+#          ::rb_matrix_num(bodnum)            number of matrices in rigid body.
+#          ::rb_mult(bodnum,matrixnum)        multiplier for matrix.
+#          ::rb_damp(bodnum,matrixnum)        damping factor for matrix.
+#          ::rb_var(bodnum,matrixnum)         variable for matrix.
+#          ::rb_coord_num(bodnum,matrixnum)   number of coordinates associated with matrix.
+#          ::rb_coord(bodnum,matrixnum,coord) coordinates
+#          ::rb_x(bodnum,matrixnum,coordnum)  x coordinate
+#          ::rb_y(bodnum,matrixnum,coordnum)  y coordinate
+#          ::rb_z(bodnum,matrixnum,coordnum   z coordinate
+#          ::rb_lbl(bodnum,matrixnum,coordnum label for coordinate triplet
 
 proc RB_Load_RBdata {args} {
     catch {unset ::rb}
     #Loop over the rigid body types in EXP file
-    foreach bodytyp [RigidBodyList] {
-             set rb($bodytyp) [ReadRigidBody $bodytyp]
+    foreach bodnum [RigidBodyList] {
+             set rb($bodnum) [ReadRigidBody $bodnum]
              #Set the number of times rigid body is mapped.
-             set ::rb_map($bodytyp) [lindex $rb($bodytyp) 0]
-
+             set ::rb_map($bodnum) [lindex $rb($bodnum) 0]
              #define the matrices
-             set rb_mat [lindex $rb($bodytyp) 1]
-             set ::rb_matrix_num($bodytyp) [llength $rb_mat]
-             for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodytyp)} {incr matrixnum} {
+             set rb_mat [lindex $rb($bodnum) 1]
+             set ::rb_matrix_num($bodnum) [llength $rb_mat]
+             for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodnum)} {incr matrixnum} {
                  set temp [lindex $rb_mat [expr $matrixnum - 1]]
-                 set ::rb_mult($bodytyp,$matrixnum) [lindex $temp 0]
-                 set ::rb_damp($bodytyp,$matrixnum) [lindex $temp 1]
-                 set ::rb_var($bodytyp,$matrixnum)  [lindex $temp 2]
+                 set ::rb_mult($bodnum,$matrixnum) [lindex $temp 0]
+                 set ::rb_damp($bodnum,$matrixnum) [lindex $temp 1]
+                 set ::rb_var($bodnum,$matrixnum)  [lindex $temp 2]
+                 if {$::rb_var($bodnum,$matrixnum) == 0} {
+                    set ::rb_varcheck($bodnum,$matrixnum) 0
+                 } else {
+                    set ::rb_varcheck($bodnum,$matrixnum) 1
+                 }
                  set coords [lindex $temp 3]
-                 set ::rb_coord_num($bodytyp,$matrixnum) [llength $coords]
+                 set ::rb_coord_num($bodnum,$matrixnum) [llength $coords]
                  #load all coordniate information for matrix matrixnum
-                 for {set coordnum 0} {$coordnum < $::rb_coord_num($bodytyp,$matrixnum)} {incr coordnum} {
-                     set ::rb_coord($bodytyp,$matrixnum,$coordnum) [lindex $coords $coordnum]
-                     set ::rb_x($bodytyp,$matrixnum,$coordnum) [lindex $::rb_coord($bodytyp,$matrixnum,$coordnum) 0]
-                     set ::rb_y($bodytyp,$matrixnum,$coordnum) [lindex $::rb_coord($bodytyp,$matrixnum,$coordnum) 0]
-                     set ::rb_z($bodytyp,$matrixnum,$coordnum) [lindex $::rb_coord($bodytyp,$matrixnum,$coordnum) 0]
-                     set ::rb_lbl($bodytyp,$matrixnum,$coordnum) [lindex $::rb_coord($bodytyp,$matrixnum,$coordnum) 0]
+                 for {set coordnum 0} {$coordnum < $::rb_coord_num($bodnum,$matrixnum)} {incr coordnum} {
+                     set ::rb_coord($bodnum,$matrixnum,$coordnum) [lindex $coords $coordnum]
+                     set ::rb_x($bodnum,$matrixnum,$coordnum) [lindex $::rb_coord($bodnum,$matrixnum,$coordnum) 0]
+                     set ::rb_y($bodnum,$matrixnum,$coordnum) [lindex $::rb_coord($bodnum,$matrixnum,$coordnum) 0]
+                     set ::rb_z($bodnum,$matrixnum,$coordnum) [lindex $::rb_coord($bodnum,$matrixnum,$coordnum) 0]
+                     set ::rb_lbl($bodnum,$matrixnum,$coordnum) [lindex $::rb_coord($bodnum,$matrixnum,$coordnum) 0]
                  }
              }
@@ -89 +164 @@
 
 ############################################
-#           ::rb_map_beginning(phase,bodytyp,mapnum)   first atom in list
-#           ::rb_map_origin(phase,bodytyp,mapnum)      origin of rigid body
-#           ::rb_map_euler(phase,bodytyp,mapnum)       euler angles of rigid body
-#           ::rb_map_positions(phase,bodytyp,mapnum)   positions
-#           ::rb_map_damping(phase,bodytyp,mapnum)     damping
-#           ::rb_map_tls(phase,bodytyp,mapnum)         tls
-#           ::rb_map_tls_var(phase,bodytyp,mapnum)
-#           ::rb_map_tls_damp(phase,bodytyp,mapnum)
-proc RB_Load_Mapdata {phase bodytyp mapnum} {
-     set rb_map [ReadRigidBodyMapping $phase $bodytyp $mapnum]
-     set ::rb_map_beginning($phase,$bodytyp,$mapnum) [lindex $rb_map 0]
-     set ::rb_map_origin($phase,$bodytyp,$mapnum) [lindex $rb_map 1]
-     set ::rb_map_euler($phase,$bodytyp,$mapnum) [lindex $rb_map 2]
-     set ::rb_map_positionvars($phase,$bodytyp,$mapnum) [lindex $rb_map 3]
-     set ::rb_map_damping($phase,$bodytyp,$mapnum) [lindex $rb_map 4]
-     set ::rb_map_tls($phase,$bodytyp,$mapnum) [lindex $rb_map 5]
-     set ::rb_map_tls_var($phase,$bodytyp,$mapnum) [lindex $rb_map 6]
-     set ::rb_map_tls_damp($phase,$bodytyp,$mapnum) [lindex $rb_map 7]
+#           ::rb_map_beginning(phase,bodnum,mapnum)   first atom in list
+#           ::rb_map_origin(phase,bodnum,mapnum)      origin of rigid body
+#           ::rb_map_euler(phase,bodnum,mapnum)       euler angles of rigid body
+#           ::rb_map_positions(phase,bodnum,mapnum)   positions
+#           ::rb_map_damping(phase,bodnum,mapnum)     damping
+#           ::rb_map_tls(phase,bodnum,mapnum)         tls
+#           ::rb_map_tls_var(phase,bodnum,mapnum)
+#           ::rb_map_tls_damp(phase,bodnum,mapnum)
+proc RB_Load_Mapdata {phase bodnum mapnum} {
+     set rb_map [ReadRigidBodyMapping $phase $bodnum $mapnum]
+     set ::rb_map_beginning($phase,$bodnum,$mapnum) [lindex $rb_map 0]
+     set ::rb_map_origin($phase,$bodnum,$mapnum) [lindex $rb_map 1]
+     set ::rb_map_euler($phase,$bodnum,$mapnum) [lindex $rb_map 2]
+     set ::rb_map_positionvars($phase,$bodnum,$mapnum) [lindex $rb_map 3]
+     set ::rb_map_damping($phase,$bodnum,$mapnum) [lindex $rb_map 4]
+     set ::rb_map_tls($phase,$bodnum,$mapnum) [lindex $rb_map 5]
+     set ::rb_map_tls_var($phase,$bodnum,$mapnum) [lindex $rb_map 6]
+     set ::rb_map_tls_damp($phase,$bodnum,$mapnum) [lindex $rb_map 7]
 }
 
@@ -156 +231 @@
      $::rb_notebook raise [$::rb_notebook page 0]
      #sets the new rigidbody number
-     set bodytyp [expr [llength [RigidBodyList]] + 1]
+     set bodnum [expr [llength [RigidBodyList]] + 1]
      #sets the phase list
      set phase $::expmap(phaselist)
@@ -167 +242 @@
 
      #initialize matrix number, multiplier and number of coordinates
-     set ::rb_matrix_num($bodytyp) 1
-     set ::rb_mult($bodytyp,1) 1.000
-
-     if {[info vars ::rb_coord_num($bodytyp,1)] == ""} {set ::rb_coord_num($bodytyp,1) 1}
+     set ::rb_matrix_num($bodnum) 1
+     set ::rb_mult($bodnum,1) 1.000
+
+     if {[info vars ::rb_coord_num($bodnum,1)] == ""} {set ::rb_coord_num($bodnum,1) 1}
 
      #set check variables to see if number of matricies or coordinates incremented.
@@ -178 +253 @@
      #building rigid body creation frames
      pack [frame $con0 -bd 2 -relief groove] -side top -pady 10
-     
-      set ::rb_loader(manual) NewBodyTypeWindow
+
+     set ::rb_loader(manual) NewBodyTypeWindow
      set ::rb_descriptor(manual) "Manual Input"
 
@@ -190 +265 @@
 
      set filecount 0
-     set ::rb_file_loader "File Descriptions"
-     grid [label $con0.lbl -text "Data Input Type: "] -row 0 -column 0
+     set ::rb_file_loader "Choose Method"
+     grid [label $con0.lbl -text "How are rigid body coordinates \n to be entered?"] -row 0 -column 0 -sticky ns
      set menu [eval tk_optionMenu $con0.filematrix ::rb_file_loader $filedescriptors]
          foreach file $filearray {
@@ -197 +272 @@
                  incr filecount
          }
-     $con0.filematrix configure -width 17
+     $con0.filematrix configure -width 50
      grid $con0.filematrix -row 0 -column 1
-
-
-     #grid [button $con0.but -text "Create from window" -width 20 -command NewBodyTypeWindow] -row 2 -column 0 -padx 5 -pady 5 -columnspan 2
-     #grid [button $con0.cartload -text "Create from file \n cartesian coordinates" -width 20 -command "RB_Cartesian_Load"] -row 0 -column 1
-     #grid [button $con0.cartz -text "Create from \n Z-Matrix" -width 20 -command "RB_Zmat_Load"] -row 1 -column 1 -padx 5 -pady 5
-     grid [button $con0.fixfrag -text "Fix Molecular \n Fragment" -width 20 -command "RB_Fixfrag_Load"] -row 1 -column 0 -padx 5 -pady 5 -columnspan 2
-
 
 }
@@ -212 +280 @@
 #procedure to create tables of cartesian coordinates
 
-proc RB_Create_Cart {bodytyp location args} {
-     if {$::rb_matrix_num($bodytyp) == $::rb_mat_num_check && $::rb_coord_num($bodytyp,1) == $::rb_atom_num_check} {return}
-     if {[catch {expr $::rb_matrix_num($bodytyp)}] == 1 || [catch {expr $::rb_coord_num($bodytyp,1)}] == 1} {return}
-     if {$::rb_matrix_num($bodytyp) != int($::rb_matrix_num($bodytyp)) || $::rb_coord_num($bodytyp,1) != int($::rb_coord_num($bodytyp,1)) } {return}
+proc RB_Create_Cart {bodnum location args} {
+     if {$::rb_matrix_num($bodnum) == $::rb_mat_num_check && $::rb_coord_num($bodnum,1) == $::rb_atom_num_check} {return}
+     if {[catch {expr $::rb_matrix_num($bodnum)}] == 1 || [catch {expr $::rb_coord_num($bodnum,1)}] == 1} {return}
+     if {$::rb_matrix_num($bodnum) != int($::rb_matrix_num($bodnum)) || $::rb_coord_num($bodnum,1) != int($::rb_coord_num($bodnum,1)) } {return}
      eval destroy [winfo children $location]
-
      foreach {top main side lbl} [MakeScrollTable $location] {}
-     set ::rb_atom_num_check $::rb_coord_num($bodytyp,1)
-     set ::rb_mat_num_check $::rb_matrix_num($bodytyp)
+     set ::rb_atom_num_check $::rb_coord_num($bodnum,1)
+     set ::rb_mat_num_check $::rb_matrix_num($bodnum)
      set col 0
      grid [label $top.multilbl -text "Matrix Multiplier"] -row 1 -column 0
      grid [label $top.damplbl -text "Damping Factor"] -row 2 -column 0
-     for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodytyp)} {incr matrixnum} {
+     for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodnum)} {incr matrixnum} {
           grid [label $top.matlbl$matrixnum -text "Matrix $matrixnum"] -row 0 -column [expr $col + 2]
-          grid [entry $top.multi$matrixnum -textvariable ::rb_mult($bodytyp,$matrixnum) -width 7 -takefocus 1] -row 1 -column [expr $col +2]
-          grid [entry $top.damp$matrixnum -textvariable ::rb_damp($bodytyp,$matrixnum) -width 7 -takefocus 1] -row 2 -column  [expr $col +2]
-          if {$::rb_mult($bodytyp,$matrixnum) == ""} {set ::rb_mult($bodytyp,$matrixnum) 1.000}
-          if {$::rb_damp($bodytyp,$matrixnum) == ""} {set ::rb_damp($bodytyp,$matrixnum) 0}
+          grid [entry $top.multi$matrixnum -textvariable ::rb_mult($bodnum,$matrixnum) -width 7 -takefocus 1] -row 1 -column [expr $col +2]
+          grid [entry $top.damp$matrixnum -textvariable ::rb_damp($bodnum,$matrixnum) -width 7 -takefocus 1] -row 2 -column  [expr $col +2]
+          if {$::rb_mult($bodnum,$matrixnum) == ""} {set ::rb_mult($bodnum,$matrixnum) 1.000}
+          if {$::rb_damp($bodnum,$matrixnum) == ""} {set ::rb_damp($bodnum,$matrixnum) 0}
 
           grid [label $main.x$matrixnum -text "X"] -row 0 -column [expr $col + 1]
@@ -238 +305 @@
      }
 
-     for {set coordnum 1} {$coordnum <= $::rb_coord_num($bodytyp,1)} {incr coordnum} {
-          grid [label $main.lbl$coordnum -text "Site $coordnum"] -row [expr $coordnum+10] -column 0
+     for {set coordnum 0} {$coordnum <= [expr $::rb_coord_num($bodnum,1) - 1]} {incr coordnum} {
+          grid [label $main.lbl$coordnum -text "Site [expr $coordnum + 1]"] -row [expr $coordnum+10] -column 0
           set col 0
-          for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodytyp)} {incr matrixnum} {
-              grid [entry $main.x($matrixnum,$coordnum) -textvariable ::rb_x($bodytyp,$matrixnum,$coordnum) -width 8 -takefocus 1] -row [expr $coordnum+10] -column [expr $col + 1]
-              if {$::rb_x($bodytyp,$matrixnum,$coordnum) == ""} {set ::rb_x($bodytyp,$matrixnum,$coordnum) 0}
-              grid [entry $main.y($matrixnum,$coordnum) -textvariable ::rb_y($bodytyp,$matrixnum,$coordnum) -width 8 -takefocus 1] -row [expr $coordnum+10] -column [expr $col + 2]
-              if {$::rb_y($bodytyp,$matrixnum,$coordnum) == ""} {set ::rb_y($bodytyp,$matrixnum,$coordnum) 0}
-              grid [entry $main.z($matrixnum,$coordnum) -textvariable ::rb_z($bodytyp,$matrixnum,$coordnum) -width 8 -takefocus 1] -row [expr $coordnum+10] -column [expr $col + 3]
-              if {$::rb_z($bodytyp,$matrixnum,$coordnum) == ""} {set ::rb_z($bodytyp,$matrixnum,$coordnum) 0}
+          for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodnum)} {incr matrixnum} {
+              grid [entry $main.x($matrixnum,$coordnum) -textvariable ::rb_x($bodnum,$matrixnum,$coordnum) -width 8 -takefocus 1] -row [expr $coordnum+10] -column [expr $col + 1]
+              if {$::rb_x($bodnum,$matrixnum,$coordnum) == ""} {set ::rb_x($bodnum,$matrixnum,$coordnum) 0}
+              grid [entry $main.y($matrixnum,$coordnum) -textvariable ::rb_y($bodnum,$matrixnum,$coordnum) -width 8 -takefocus 1] -row [expr $coordnum+10] -column [expr $col + 2]
+              if {$::rb_y($bodnum,$matrixnum,$coordnum) == ""} {set ::rb_y($bodnum,$matrixnum,$coordnum) 0}
+              grid [entry $main.z($matrixnum,$coordnum) -textvariable ::rb_z($bodnum,$matrixnum,$coordnum) -width 8 -takefocus 1] -row [expr $coordnum+10] -column [expr $col + 3]
+              if {$::rb_z($bodnum,$matrixnum,$coordnum) == ""} {set ::rb_z($bodnum,$matrixnum,$coordnum) 0}
               grid [label $main.b($matrixnum,$coordnum) -text "    "] -row [expr $coordnum+10]  -column [expr $col +4]
               incr col 4
@@ -257 +324 @@
 # Procedure to save new rigid body to EXP file.
 
-proc RB_Create_Save {bodytyp args} {
+proc RB_Create_Save {bodnum args} {
      set temp_mat ""
      set temp_car ""
@@ -263 +330 @@
      set temp_car_group ""
      set total ""
-#     puts $::::rb_coord_num($bodytyp,1)
-     for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodytyp)} {incr matrixnum} {
-         lappend temp_mat $::rb_mult($bodytyp,$matrixnum)
-     }
-
-     for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodytyp)} {incr matrixnum} {
-         for {set coordnum 1} {$coordnum <= $::rb_coord_num($bodytyp,1)} {incr coordnum} {
-                  set temp_cart_triplet "$::rb_x($bodytyp,$matrixnum,$coordnum) $::rb_y($bodytyp,$matrixnum,$coordnum) $::rb_z($bodytyp,$matrixnum,$coordnum)"
+#     puts $::::rb_coord_num($bodnum,1)
+     for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodnum)} {incr matrixnum} {
+         lappend temp_mat $::rb_mult($bodnum,$matrixnum)
+     }
+
+     for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodnum)} {incr matrixnum} {
+         for {set coordnum 0} {$coordnum < $::rb_coord_num($bodnum,1)} {incr coordnum} {
+                  set temp_cart_triplet "$::rb_x($bodnum,$matrixnum,$coordnum) $::rb_y($bodnum,$matrixnum,$coordnum) $::rb_z($bodnum,$matrixnum,$coordnum)"
                   lappend temp $temp_cart_triplet
          }
          lappend temp_car $temp
      }
-#     puts "sites: $::rb_coord_num($bodytyp,1)"
+#     puts "sites: $::rb_coord_num($bodnum,1)"
 #     puts "matrix multiplier:  $temp_mat"
 #     puts "cartesian coords:   $temp_car"
@@ -283 +350 @@
      destroy .nbt
      RB_Load_RBdata
-     RB_Control_Panel $bodytyp
+     RB_Control_Panel $bodnum
 }
 
@@ -289 +356 @@
 # Procedures to delete rigid bodies
 
-proc RB_Delete_Body {bodytyp location args} {
+proc RB_Delete_Body {bodnum location args} {
      destroy $location.delete
      set really $location.delete
      toplevel $really
-#     putontop $really
+     putontop $really
      wm title $really "Delete Rigid Body"
-     #wm geometry $really 250x250+10+10
-     grid [label $really.lbl -text "Confirm \n Is rigid body $bodytyp to be deleted?"] -row 0 -column 0 -columnspan 2 -pady 15
-
-     grid [button $really.save -text "Delete" -bg red -command "RB_Delete_Body_Confirm $bodytyp $location.delete"] \
+     grid [label $really.lbl -text "Confirm \n Is rigid body $bodnum to be deleted?"] -row 0 -column 0 -columnspan 2 -pady 15
+     grid [button $really.save -text "Delete" -bg red -command "RB_Delete_Body_Confirm $bodnum $location.delete"] \
           -row 1 -column 0 -padx 5 -pady 5
-     grid [button $really.abort -text "Abort" -bg green -command "RB_Control_Panel $bodytyp"] -row 1 -column 1 \
+     grid [button $really.abort -text "Abort" -bg green -command "RB_Populate $::rb_notebook $bodnum; \
+     $::rb_notebook raise rb_body$bodnum"] -row 1 -column 1 \
           -padx 5 -pady 5
 }
 
-proc RB_Delete_Body_Confirm {bodytyp location args} {
+proc RB_Delete_Body_Confirm {bodnum location args} {
 
  #   unmap all instances of the rigid body
-     foreach p $::expmap(phaselist) {
-             foreach map [RigidBodyMappingList $p $bodytyp] {
-                     UnMapRigidBody $p $bodytyp $map
+     foreach phase $::expmap(phaselist) {
+             foreach mapnum [RigidBodyMappingList $phase $bodnum] {
+                     UnMapRigidBody $pphase $bodnum $mapnum
              }
-#       lappend pagelist rb_body$x
-     }
-#    delete the rigid body
-#     puts "delete rigid body number $bodytyp"
-     DeleteRigidBody $bodytyp
-#     puts "destroy location $location"
+     }
+#    puts "delete rigid body number $bodnum"
+     DeleteRigidBody $bodnum
+#    puts "destroy location $location"
      destroy $location
 #    increment expgui
@@ -327 +391 @@
 # Procedure to populate notebook pages
 
-proc RB_Populate {rb_notebook bodytyp args} {
+proc RB_Populate {rb_notebook bodnum args} {
      RB_Load_RBdata
-     set ::rb_panel $bodytyp
+     set ::rb_panel $bodnum
      set phaselist $::expmap(phaselist)
      # set notebook frame
-     set pane [$rb_notebook getframe rb_body$bodytyp]
+     set pane [$rb_notebook getframe rb_body$bodnum]
      eval destroy [winfo children $pane]
      set con $pane.con
@@ -338 +402 @@
 
      #Rigid body mapping control panel along with matrix multipliers and damping factor labels
-     grid [label  $con.rb_num -text "Rigid Body Type $bodytyp"] -row 0 -column 0 -padx 5 -pady 5
-     grid [button $con.rb_newmap -text "Map Body $bodytyp" -command "RB_Map_New $bodytyp" -width 18] -row 0 -column 1 -padx 5 -pady 5
-     grid [button $con.rb_unmap -text "Unmap Body $bodytyp" -command "RB_Unmap $bodytyp" -width 18] -row 0 -column 2 -padx 5 -pady 5
-     button $con.rb_delete -text "Delete Body $bodytyp" -command "RB_Delete_Body $bodytyp $con.rb_delete" -width 18
+     grid [label  $con.rb_num -text "Rigid Body Type $bodnum"] -row 0 -column 0 -padx 5 -pady 5
+     grid [button $con.rb_newmap -text "Map Body $bodnum" -command "RB_Map_New $bodnum" -width 18] -row 0 -column 1 -padx 5 -pady 5
+     grid [button $con.rb_unmap -text "Unmap Body $bodnum" -command "RB_Unmap $bodnum" -width 18] -row 0 -column 2 -padx 5 -pady 5
+     button $con.rb_delete -text "Delete Body $bodnum" -command "RB_Delete_Body $bodnum $con.rb_delete" -width 18
      grid   $con.rb_delete -row 4 -column 2 -padx 5 -pady 5
-
 
      grid [label $con.rb_mlbl1 -text "Matrix"] -row 1 -column 0
      grid [label $con.rb_mlbl2 -text "Multiplier"] -row 2 -column 0
      grid [label $con.rb_mlbl3 -text "Damping Factor"] -row 3 -column 0
-     grid [button $con.plot -text "Plot Rigid Body" -command "PlotRBtype $bodytyp" -width 18] -row 4 -column 0
+     grid [button $con.plot -text "Plot Rigid Body" -command "PlotRBtype $bodnum" -width 18] -row 4 -column 0
 
      set matrixnum 0
-     for {set mnum 1} {$mnum <= $::rb_matrix_num($bodytyp)} {incr mnum} {
+     for {set mnum 1} {$mnum <= $::rb_matrix_num($bodnum)} {incr mnum} {
         incr matrixnum
         grid [label $con.rb_mm$mnum   -text "$mnum"]                -row 1 -column $matrixnum
-        grid [label $con.rb_mult$mnum -text "$::rb_mult($bodytyp,$mnum)"] -row 2 -column $matrixnum
-        grid [label $con.rb_damp$mnum -text "$::rb_damp($bodytyp,$mnum)"] -row 3 -column $matrixnum
-     }
-
-     button $con.rb_vmatrix -text "Edit Matrix" -command "RB_Edit_Matrix $bodytyp" -width 18
+        grid [label $con.rb_mult$mnum -text "$::rb_mult($bodnum,$mnum)"] -row 2 -column $matrixnum
+        grid [label $con.rb_damp$mnum -text "$::rb_damp($bodnum,$mnum)"] -row 3 -column $matrixnum
+     }
+
+     button $con.rb_vmatrix -text "Edit Matrix" -command "RB_Edit_Matrix $bodnum" -width 18
      grid   $con.rb_vmatrix -row 4 -column 1 -padx 5 -pady 5
      grid [button $con.refine -text "Refinement \n Flags" -command "RB_Refine_Con" -width 18 ] -row 5 -column 1
@@ -375 +438 @@
      grid [label $main.rb_euler_y -text "y"] -row 1 -column 7
      grid [label $main.rb_euler_z -text "z"] -row 1 -column 8
-#     grid [label $main.rb_opt     -text "Refine"] -row 1 -column 9 -padx 8
      set col 11
-     for {set coordnum 1} {$coordnum <= $::rb_coord_num($bodytyp,1)} {incr coordnum} {
+     for {set coordnum 1} {$coordnum <= $::rb_coord_num($bodnum,1)} {incr coordnum} {
         label $main.rb_site$coordnum -text "$coordnum"
         grid $main.rb_site$coordnum -row 1 -column $col -padx 5
@@ -387 +449 @@
      foreach phase $phaselist {
              incr row
-             foreach mapnum [RigidBodyMappingList $phase $bodytyp] {
+             foreach mapnum [RigidBodyMappingList $phase $bodnum] {
                       set row [expr $row + $mapnum]
-                      RB_Load_Mapdata $phase $bodytyp $mapnum
+                      RB_Load_Mapdata $phase $bodnum $mapnum
                       grid [label $main.rb_map$phase$mapnum -text "$mapnum"] -row $row -column 1
                       grid [label $main.rb_cb$phase$mapnum -text $phase] -row $row -column 2
-                      set origin $::rb_map_origin($phase,$bodytyp,$mapnum)
+                      set origin $::rb_map_origin($phase,$bodnum,$mapnum)
 
                       grid [label $main.rb_x$phase$mapnum   -text "[format %1.3f [lindex $origin 0]]"] -row $row -column 3 -padx 5
                       grid [label $main.rb_y$phase$mapnum   -text "[format %1.3f [lindex $origin 1]]"] -row $row -column 4 -padx 5
                       grid [label $main.rb_z$phase$mapnum   -text "[format %1.3f [lindex $origin 2]]"] -row $row -column 5 -padx 5
-                      set euler $::rb_map_euler($phase,$bodytyp,$mapnum)
+                      set euler $::rb_map_euler($phase,$bodnum,$mapnum)
                       for {set j 0} {$j < 3} {incr j} {
                                   set euler1 [lindex $euler $j]
@@ -404 +466 @@
                                   label $main.rb_euler_$phase$mapnum$axis -text "[format %1.2f $angle]"
                       }
-#                      grid [button $main.rb_tls$phase$mapnum -text "Refine" -command "RB_Refine_Con" -width 7] -row $row -column 9
-                       grid [label $main.rb_tls$phase$mapnum -text "     "] -row $row -column 9
+
+                      grid [label $main.rb_tls$phase$mapnum -text "     "] -row $row -column 9
                       set q 1
                       grid $main.rb_euler_$phase$mapnum$q -row $row -column 6  -padx 5
@@ -413 +475 @@
                       grid $main.rb_euler_$phase$mapnum$q -row $row -column 8 -padx 5
                       set col 11
-                      set atomnum $::rb_map_beginning($phase,$bodytyp,$mapnum)
-                      for {set j 1} {$j <=$::rb_coord_num($bodytyp,1)} {incr j} {
+                      set atomnum $::rb_map_beginning($phase,$bodnum,$mapnum)
+                      for {set coordnum 1} {$coordnum <=$::rb_coord_num($bodnum,1)} {incr coordnum} {
                           set atom [atominfo $phase $atomnum label]
-                          grid [label $main.rb_site$phase$mapnum$j -text "$atom"] -row $row -column $col -padx 5
+                          grid [label $main.rb_site$phase$mapnum$coordnum -text "$atom"] -row $row -column $col -padx 5
                           incr atomnum
                           incr col
@@ -426 +488 @@
 }
 
+proc DisplayRB {} {     ;# called each time the panel is raised
+    eval destroy [winfo children $::expgui(rbFrame)]
+     RB_Load_RBdata
+     RB_Control_Panel 0
+    #label $::expgui(rbFrame).l -text "RB Parameters"
+    #grid $::expgui(rbFrame).l -column 1 -row 1
+    ResizeNotebook
+}
+
+proc MakeRBPane {} {     ;# called to create the panel intially
+#    label $::expgui(rbFrame).l -text "RB Parameters"
+#    grid $::expgui(rbFrame).l -column 1 -row 1
+#    ResizeNotebook
+}
 
 #######################################################################
@@ -431 +507 @@
 # not updated
 
-proc RB_Map_New {bodytyp args} {
-    catch {unset ::rb_finput}
-    set ::rb_finput ""
-    set ::body_type $bodytyp
+proc RB_Map_New {bodnum args} {
+    catch {unset ::rb_firstatom}
+    set ::rb_firstatom ""
+    set ::body_type $bodnum
     catch {destroy .newmap}
     set nm .newmap
     toplevel $nm
     putontop $nm
-    wm title $nm "Map Rigid Body #$bodytyp"
+    wm title $nm "Map Rigid Body #$bodnum"
 
     foreach item [trace vinfo ::rb_phase] {
@@ -446 +522 @@
 
     set ::rb_phase [lindex $::expmap(phaselist) 0]
-    set nmap [expr $::rb_map($bodytyp) + 1]
+    set nmap [expr $::rb_map($bodnum) + 1]
     eval tk_optionMenu $nm.pinput ::rb_phase $::expmap(phaselist)
     grid [label $nm.phase -text "Phase: "] -row 3 -column 1
@@ -452 +528 @@
     grid [label $nm.origin -text "input origin in fractional coordinates: "] -row 6 -column 1
     grid [label $nm.euler -text "input Euler angles: "] -row 7 -column 1
-    grid [entry $nm.finputm -textvariable ::rb_finput -width 8 -takefocus 1] -row 4 -column 2
-
-    foreach item [trace vinfo ::rb_finput] {
-            eval trace vdelete ::rb_finput $item
-    }
-    trace variable ::rb_finput w "RB_Atom_List \$::rb_phase \$::rb_finput $nm $bodytyp 1"
-
-    grid [button $nm.finput -text "list allowed" -command "RB_Choose_Atom $bodytyp"] -row 4 -column 3
+    grid [entry $nm.finputm -textvariable ::rb_firstatom -width 8 -takefocus 1] -row 4 -column 2
+
+    foreach item [trace vinfo ::rb_firstatom] {
+            eval trace vdelete ::rb_firstatom $item
+    }
+    trace variable ::rb_firstatom w "RB_Atom_List \$::rb_phase \$::rb_firstatom $nm $bodnum"
+
+    grid [button $nm.finput -text "list allowed" -command "RB_Choose_Atom $bodnum"] -row 4 -column 3
     grid [label $nm.o1l -text "x"] -row 5 -column 2
     grid [label $nm.o2l -text "y"] -row 5 -column 3
     grid [label $nm.o3l -text "z"] -row 5 -column 4
+
+    set ::origin1 0
+    set ::origin2 0
+    set ::origin3 0
+    set ::euler1 0
+    set ::euler2 0
+    set ::euler3 0
+
     grid [entry $nm.o1 -width 8 -textvariable ::origin1 -takefocus 1] -row 6 -column 2
     grid [entry $nm.o2 -width 8 -textvariable ::origin2 -takefocus 1] -row 6 -column 3
@@ -473 +557 @@
 
     grid [frame $nm.p] -row 8 -column 1 -columnspan 4 -sticky e
-    grid [button $nm.p.fit -text "Fit rigid body to phase" -command "FitBody2coords $bodytyp $nm"] -row 0 -column 1
-    grid [button $nm.p.plot -text "Plot rigid body & phase" -command "PlotStrBody $bodytyp $nm"] -row 1 -column 1
+    grid [button $nm.p.fit -text "Fit rigid body to phase" -command "RB_FitBody2Coords $bodnum $nm; RB_View_RMS $nm"] -row 0 -column 1
+    grid [button $nm.p.plot -text "Plot rigid body & phase" -command "RB_PlotStrBody $bodnum $nm"] -row 1 -column 1
     grid [label $nm.p.l -text "Bonds: "] -row 1 -column 2
     grid [entry $nm.p.e] -row 1 -column 3
@@ -482 +566 @@
     grid [frame $nm.l] -row 9 -column 2 -columnspan 3
     grid [button $nm.l.s -text "map update" -width 12 -command {RB_Write_Map}] -column 1 -row 1
-    grid [button $nm.l.q -text "Quit" -width 6 -command "destroy $nm"] -column 2  -row 1
+    grid [button $nm.l.q -text "Abort" -width 6 -command "destroy $nm"] -column 2  -row 1
 
     foreach item [trace vinfo ::rb_phase] {
             eval trace vdelete ::rb_phase $item
     }
-    trace variable ::rb_phase w "RB_ProcessPhase $bodytyp"
-
-
+    trace variable ::rb_phase w "RB_ProcessPhase $bodnum"
+}
+
+proc RB_View_RMS {address args} {
+     set addrms $address.rms
+     catch {destroy $addrms}
+     grid [frame $addrms -bd 2] -row 5 -column 8 -columnspan 99 -rowspan 99
+     set row 1
+
+     grid [label $addrms.atomlbl -text "   atom"] -row 0 -column 0
+     grid [label $addrms.rmslbl -text "\t rms"] -row 0 -column 1
+     foreach i $::rb_atom_rms {
+             set atom [lindex $i 0]
+             set temp [lindex $i 1]
+             set rms [format %.3f $temp]
+             set id [string tolower $atom]
+             grid [label $addrms.$id$row -text "   $atom"] -row $row -column 0
+             grid [label $addrms.rms$id$row -text "\t $rms"] -row $row -column 1
+             incr row
+     }
 }
 
@@ -496 +597 @@
 # not updated
 
-proc RB_Choose_Atom {bodytyp args} {
-#     set ::rb_finput ""
+proc RB_Choose_Atom {bodnum args} {
     set phase $::rb_phase
     # get the number of atoms in this type of body
-    set natoms [llength [lindex [lindex [lindex [ReadRigidBody $bodytyp] 1] 0] 3]]
+    set natoms [llength [lindex [lindex [lindex [ReadRigidBody $bodnum] 1] 0] 3]]
     set atomlist [RigidStartAtoms $::rb_phase $natoms]
     if {[llength $atomlist] == 0} {
-        RB_ProcessPhase $bodytyp
+        RB_ProcessPhase $bodnum
         return
     }
@@ -516 +616 @@
      foreach atom $atomlist {
         set label "[atominfo $phase $atom label] \($atom\)"
-# fix next line need global variable to send.
-#        button $main.$atom -text "$label" -command "set ::rb_finput [list $label]; destroy $ca"
-        button $main.$atom -text $label -command "set ::rb_finput $atom; destroy $ca"
+        button $main.$atom -text $label -command "set ::rb_firstatom $atom; destroy $ca"
         incr row
         if {$row > 5} {
@@ -533 +631 @@
 }
 
-
-
 ##########################################################
 ##########################################################
 
-  
-proc FitBody2coords {rbtype menu} {
+proc RB_FitBody2Coords {bodnum menu} {
     set warn ""
     foreach i {1 2 3} lbl {x y z} {
@@ -555 +650 @@
         }
     }
-    if {[catch {expr $::rb_finput}]} {
+    if {[catch {expr $::rb_firstatom}]} {
         append warn "\tError in 1st atom number\n"
     }
@@ -570 +665 @@
         lappend cell [phaseinfo $phase $p]
     }
-    set coords [RB2cart [lindex [ReadRigidBody $rbtype] 1]]
+    set coords [RB2cart [lindex [ReadRigidBody $bodnum] 1]]
     set natom [llength $coords]
-    set firstind [lsearch $::expmap(atomlist_$phase) $::rb_finput]
+    set firstind [lsearch $::expmap(atomlist_$phase) $::rb_firstatom]
     set atoms [lrange \
                    [lrange $::expmap(atomlist_$phase) $firstind end] \
@@ -598 +693 @@
     }
     # show deviations
-    
+
+    set ::rb_atom_rms ""
     foreach atom $atoms rms $rmsbyatom {
         puts "[atominfo $phase $atom label]\t$rms"
+        lappend ::rb_atom_rms "[atominfo $phase $atom label] $rms"
     }
     #puts "CalcBody $Euler $cell $coords $origin"
     #puts $coords
     #puts $frcoords
-    #DRAWxtlPlotRBFit $frcoords $phase $::rb_finput 0 $bondlist $bondlist
+    #DRAWxtlPlotRBFit $frcoords $phase $::rb_firstatom 0 $bondlist $bondlist
  }
 
-proc PlotStrBody {rbtype menu} {
+proc RB_PlotStrBody {bodnum menu} {
     set warn ""
     foreach i {1 2 3} lbl {x y z} {
@@ -618 +715 @@
         }
     }
-    if {[catch {expr $::rb_finput}]} {
+    if {[catch {expr $::rb_firstatom}]} {
         append warn "\tError in 1st atom number\n"
     }
@@ -649 +746 @@
         lappend cell [phaseinfo $phase $p]
     }
-    set coords [RB2cart [lindex [ReadRigidBody $rbtype] 1]]
+    set coords [RB2cart [lindex [ReadRigidBody $bodnum] 1]]
     set frcoords [CalcBody $Euler $cell $coords $origin]
     #puts "CalcBody $Euler $cell $coords $origin"
     #puts $coords
     #puts $frcoords
-    DRAWxtlPlotRBFit $frcoords $phase $::rb_finput 0 $bondlist $bondlist
+    DRAWxtlPlotRBFit $frcoords $phase $::rb_firstatom 0 $bondlist $bondlist
  }
 #
 
 proc RB_Write_Map {args} {
+   if {$::rb_firstatom == ""} {
+      MyMessageBox -title "warning" -message "The first atom for the rigid body must be choosen to update mapping"
+      return
+   }
    set origin "$::origin1 $::origin2 $::origin3"
    set euler "$::euler1 $::euler2 $::euler3"
 #   puts "phase = $::rb_phase"
-#   puts "bodytyp = $::body_type"
-#   puts "firstatom = $::rb_finput"
+#   puts "bodnum = $::body_type"
+#   puts "firstatom = $::rb_firstatom"
 #   puts "position = $origin"
 #   puts "Euler = $euler"
-   MapRigidBody $::rb_phase $::body_type $::rb_finput $origin $euler
+   MapRigidBody $::rb_phase $::body_type $::rb_firstatom $origin $euler
    incr ::rb_map($::body_type)
    incr ::expgui(changed)
@@ -672 +773 @@
    $::rb_notebook raise [$::rb_notebook page end]
    $::rb_notebook raise $curpage
-#   RB_Control_Panel $::body_type
    destroy .newmap
    RunRecalcRBCoords
    incr ::expgui(changed)
-   RB_Control_Panel $::body_type
-
-}
-
-proc RB_Atom_List {phase atomnum address x y args} {
+   RB_Populate $::rb_notebook $::body_type
+   $::rb_notebook raise rb_body$::body_type
+}
+
+proc RB_Atom_List {phase atomnum address bodnum args} {
      foreach w [winfo children $address] {
              if {[string first ".atom" $w] != -1} {destroy $w}
@@ -686 +786 @@
      set col 8
     if {$atomnum == ""} return
-     grid [label $address.atomlbl -text "Atoms Mapped to Rigid Body"] -row 3 -column 8 -columnspan 99
+    grid [label $address.atomlbl -text "Atoms Mapped to Rigid Body"] -row 3 -column 8 -columnspan 99
     # get the number of atoms in this type of body
-    set natoms [llength [lindex [lindex [lindex [ReadRigidBody $x] 1] 0] 3]]
+    set natoms [llength [lindex [lindex [lindex [ReadRigidBody $bodnum] 1] 0] 3]]
     set atoms [RigidStartAtoms $phase $natoms]
     if {[lsearch $atoms $atomnum] == -1} {
@@ -698 +798 @@
     foreach j [lrange $atoms 0 [expr {$natoms - 1}]] {
         set atom [atominfo $phase $j label]
-        grid [label $address.atom$phase$x$j -text $atom] -row 4 -column $col
+        grid [label $address.atom$phase$bodnum$j -text $atom] -row 4 -column $col
         incr col
      }
 }
 
-proc RB_ProcessPhase {rbnum args} {
+proc RB_ProcessPhase {bodnum args} {
     if {$::rb_phase == ""} {
         set atoms {}
     } else {
         # get the number of atoms in this type of body
-        set natoms [llength [lindex [lindex [lindex [ReadRigidBody $rbnum] 1] 0] 3]]
+        set natoms [llength [lindex [lindex [lindex [ReadRigidBody $bodnum] 1] 0] 3]]
 
         set atoms [RigidStartAtoms $::rb_phase $natoms]
@@ -726 +826 @@
 }
 
-proc RB_Unmap {x args} {
-    catch {unset ::rb_finput}
-    set ::rb_finput ""
-    set ::body_type $x
+proc RB_Unmap {bodnum args} {
+    catch {unset ::rb_firstatom}
+    set ::rb_firstatom ""
+    set ::body_type $bodnum
     catch {destroy .unmap}
     set um .unmap
     toplevel $um
     putontop $um
-    wm title $um "Map Rigid Body #$x"
+    wm title $um "Map Rigid Body #$bodnum"
     set ::phase 1
-    set umap $::rb_map($x)
+    set umap $::rb_map($bodnum)
 #    eval tk_optionMenu $um.pinput ::rb_phase $::expmap(phaselist)
 #    grid [label $um.phase -text "Phase: "] -row 3 -column 1
 #    grid $um.pinput -row 3 -column 2
 
-    set mapnumber $::rb_map($x)
+    set mapnumber $::rb_map($bodnum)
     set unpane $um.pane
     foreach {top main side lbl} [MakeScrollTable $um] {}
@@ -747 +847 @@
     grid [label $main.map -text "map"] -row 1 -column 1 -padx 5
     grid [label $main.ph -text "Phase"] -row 1 -column 2 -padx 5
-    set y $::rb_matrix_num($x)
-    for {set z 1} {$z <= $::rb_coord_num($x,$y)} {incr z} {
-        label $main.rb_site$z -text "Site $z"
-        grid $main.rb_site$z -row 1 -column [expr 2 + $z]
+    set matrixnum $::rb_matrix_num($bodnum)
+    for {set coordnum 1} {$coordnum <= $::rb_coord_num($bodnum,$matrixnum)} {incr coordnum} {
+        label $main.rb_site$coordnum -text "Site $coordnum"
+        grid $main.rb_site$coordnum -row 1 -column [expr 2 + $coordnum]
     }
     set row 2
-    foreach p $::expmap(phaselist) {
+    foreach phase $::expmap(phaselist) {
         incr row
-        foreach z [RigidBodyMappingList $p $x] {
-                set row [expr $row + $z]
-                RB_Load_Mapdata $p $x $z
-                checkbutton $main.unmap$p$z -variable ::rb_unmap($p,$x,$z)
-                grid $main.unmap$p$z -row $row -column 0
-                grid [label $main.rb_map$p$z -text "$z"] -row $row -column 1
-                grid [label $main.rb_cb$p$z -text $p] -row $row -column 2
-                      set atomnum $::rb_map_beginning($p,$x,$z)
+        foreach coordnum [RigidBodyMappingList $phase $bodnum] {
+                set row [expr $row + $coordnum]
+                RB_Load_Mapdata $phase $bodnum $coordnum
+                checkbutton $main.unmap$phase$coordnum -variable ::rb_unmap($phase,$bodnum,$coordnum)
+                grid $main.unmap$phase$coordnum -row $row -column 0
+                grid [label $main.rb_map$phase$coordnum -text "$coordnum"] -row $row -column 1
+                grid [label $main.rb_cb$phase$coordnum -text $phase] -row $row -column 2
+                      set atomnum $::rb_map_beginning($phase,$bodnum,$coordnum)
                       set col 3
-                      for {set j 1} {$j <=$::rb_coord_num($x,$y)} {incr j} {
-                          set atom [atominfo $p $atomnum label]
-                          grid [label $main.rb_site$p$z$j -text "$atom"] -row $row -column $col
+                      for {set j 1} {$j <=$::rb_coord_num($bodnum,$matrixnum)} {incr j} {
+                          set atom [atominfo $phase $atomnum label]
+                          grid [label $main.rb_site$phase$coordnum$j -text "$atom"] -row $row -column $col
                           incr atomnum
                           incr col
@@ -776 +876 @@
 
      grid [frame $um.update -bd 2 -relief groove] -row 0 -column 1 -pady 10
-     button $um.update.con -text "Update Rigid Body Mapping" -command "RB_unmap_delete $um $x"
-     button $um.update.quit -text "Quit" -command "destroy $um"
+     button $um.update.con -text "Update Rigid Body Mapping" -command "RB_unmap_delete $um $bodnum"
+     button $um.update.abort -text "Abort" -command "destroy $um"
      grid $um.update.con -row 0 -column 0 -padx 5 -pady 5
-     grid $um.update.quit -row 0 -column 1
+     grid $um.update.abort -row 0 -column 1
      incr ::expgui(changed)
 
-#     UnMapRigidBody $phase $bodytyp $mapnum
-#     incr ::expgui(changed)
-#     RB_Control_Panel $bodytyp
-}
-
-proc RB_unmap_delete {panel x args} {
+}
+
+proc RB_unmap_delete {panel bodnum args} {
 #     puts $panel
-     foreach p $::expmap(phaselist) {
-        foreach z [RigidBodyMappingList $p $x] {
-                if {$::rb_unmap($p,$x,$z) == 1} {
-                   UnMapRigidBody $p $x $z
+     foreach phase $::expmap(phaselist) {
+        foreach mapnum [RigidBodyMappingList $phase $bodnum] {
+                if {$::rb_unmap($phase,$bodnum,$mapnum) == 1} {
+                   UnMapRigidBody $phase $bodnum $mapnum
                 }
         }
@@ -798 +895 @@
         destroy $panel
         set curpage [$::rb_notebook raise]
-        $::rb_notebook raise [$::rb_notebook page end]
-        $::rb_notebook raise $curpage
-        RB_Control_Panel $x
+        RB_Populate $::rb_notebook $bodnum
+        $::rb_notebook raise rb_body$bodnum
      }
 }
@@ -824 +920 @@
      grid [button $sm.dec -text "\u2193" -command "RB_Sort_Inc $bodnum dec"] -row 2 -column 1
 
-     grid [button $um.update -text "Update Matrix Info" -bg green -command "RB_Matrix_Update $bodnum"] -row 0 -column 0
+     grid [button $um.update -text "Update Matrix Info" -bg green -command "RB_Matrix_Update $bodnum"] -row 0 -column 0 -padx 5
  #    grid [button $um.sort -text "Sort Matrix Info" -command "RB_Cart_Sort $bodnum"] -row 0 -column 1
-     grid [button $um.abort -text "Abort" -command "destroy $em"] -row 0 -column 2
-
-     grid [label $vm.lbldamp -text "Matrix Multiplier"] -row 3 -column 2
-     grid [label $vm.lblvar -text "Damping Factor"] -row 4 -column 2
+     grid [button $um.abort -text "Abort" -width 18 -command "destroy $em"] -row 0 -column 2 -padx 5
+     grid [button $um.print -text "Save Cartesian \n Coordinates to File" -command "RB_CartesianTextFile $bodnum"] -row 1 -column 0 -pady 5
+
+     grid [label $vm.lblmm -text "Matrix Multiplier"] -row 3 -column 2
+     grid [label $vm.lbldamp -text "Damping Factor"] -row 4 -column 2
+     grid [label $vm.lblvar -text "Refine Multiplier"] -row 5 -column 2
 
      set w 1
-     grid [label $vm.site -text "sort"] -row 5 -column 0 -columnspan 2
+     grid [label $vm.site -text "sort"] -row 6 -column 0 -columnspan 2
 
      for {set z 0} {$z < $::rb_coord_num($bodnum,$w)} {incr z} {
-         grid [checkbutton $vm.sort$z -variable ::rb_sort($z)] -row [expr $z + 6] -column 1
-         grid [label $vm.lbls$z -text "Site [expr $z+ 1]"] -row [expr $z+6] -column 2
+         grid [checkbutton $vm.sort$z -variable ::rb_sort($z)] -row [expr $z + 7] -column 1
+         grid [label $vm.lbls$z -text "Site [expr $z+ 1]"] -row [expr $z+7] -column 2
      }
      set col 3
@@ -843 +941 @@
          grid [entry $vm.mult$i -textvariable ::rb_mult($bodnum,$i) -width 8 -takefocus 1] -row 3 -column [expr $col + 1]
          grid [entry $vm.damp$i -textvariable ::rb_damp($bodnum,$i) -width 8 -takefocus 1 -state disable] -row 4 -column [expr $col + 1]
-
-         grid [label $vm.x$i -text "X"] -row 5 -column [expr $col]
-         grid [label $vm.y$i -text "Y"] -row 5 -column [expr $col + 1]
-         grid [label $vm.z$i -text "Z"] -row 5 -column [expr $col + 2]
+         grid [checkbutton $vm.var$i -variable ::rb_varcheck($bodnum,$i) -text $::rb_var($bodnum,$i) -state disable -command ""] -row 5 -column [expr $col +1]
+
+         grid [label $vm.x$i -text "X"] -row 6 -column [expr $col]
+         grid [label $vm.y$i -text "Y"] -row 6 -column [expr $col + 1]
+         grid [label $vm.z$i -text "Z"] -row 6 -column [expr $col + 2]
          for {set j 0} {$j < $::rb_coord_num($bodnum,$w)} {incr j} {
 #             puts $::rb_coord($bodnum,$i,$j)
-             set ::x($i,$j) [lindex $::rb_coord($bodnum,$i,$j) 0]
-             set ::y($i,$j) [lindex $::rb_coord($bodnum,$i,$j) 1]
-             set ::z($i,$j) [lindex $::rb_coord($bodnum,$i,$j) 2]
-             set ::lbl($i,$j) [lindex $::rb_coord($bodnum,$i,$j) 3]
-
-             grid [entry $vm.lblcx$i$j -textvariable ::x($i,$j) -width 8 -takefocus 1] -row [expr $j+6] -column [expr $col]
-             grid [entry $vm.lblcy$i$j -textvariable ::y($i,$j) -width 8 -takefocus 1] -row [expr $j+6] -column [expr $col + 1]
-             grid [entry $vm.lblcz$i$j -textvariable ::z($i,$j) -width 8 -takefocus 1] -row [expr $j+6] -column [expr $col + 2]
+
+              set ::rb_x($bodnum,$i,$j) [lindex $::rb_coord($bodnum,$i,$j) 0]
+              set ::rb_y($bodnum,$i,$j) [lindex $::rb_coord($bodnum,$i,$j) 1]
+              set ::rb_z($bodnum,$i,$j) [lindex $::rb_coord($bodnum,$i,$j) 2]
+              set ::rb_lbl($bodnum,$i,$j) [lindex $::rb_coord($bodnum,$i,$j) 3]
+
+             grid [entry $vm.lblcx$i$j -textvariable ::rb_x($bodnum,$i,$j) -width 8 -takefocus 1] -row [expr $j+7] -column [expr $col]
+             grid [entry $vm.lblcy$i$j -textvariable ::rb_y($bodnum,$i,$j) -width 8 -takefocus 1] -row [expr $j+7] -column [expr $col + 1]
+             grid [entry $vm.lblcz$i$j -textvariable ::rb_z($bodnum,$i,$j) -width 8 -takefocus 1] -row [expr $j+7] -column [expr $col + 2]
              grid [label $vm.lblcb$i$j -text "    "] -row [expr  $j+6] -column [expr $col + 3]
          }
@@ -896 +996 @@
              if {$dir == "inc"} {set line1 [expr $sort - 1]}
              if {$dir == "dec"} {set line1 [expr $sort + 1]}
-             set x1dum $::x($i,$line1)
-             set y1dum $::y($i,$line1)
-             set z1dum $::z($i,$line1)
-             set ::x($i,$line1) $::x($i,$sort)
-             set ::y($i,$line1) $::y($i,$sort)
-             set ::z($i,$line1) $::z($i,$sort)
-             set ::x($i,$sort) $x1dum
-             set ::y($i,$sort) $y1dum
-             set ::z($i,$sort) $z1dum
+             set x1dum $::rb_x($bodnum,$i,$line1)
+             set y1dum $::rb_y($bodnum,$i,$line1)
+             set z1dum $::rb_z($bodnum,$i,$line1)
+             set ::rb_x($bodnum,$i,$line1) $::rb_x($bodnum,$i,$sort)
+             set ::rb_y($bodnum,$i,$line1) $::rb_y($bodnum,$i,$sort)
+             set ::rb_z($bodnum,$i,$line1) $::rb_z($bodnum,$i,$sort)
+             set ::rb_x($bodnum,$i,$sort) $x1dum
+             set ::rb_y($bodnum,$i,$sort) $y1dum
+             set ::rb_z($bodnum,$i,$sort) $z1dum
 
              set ::rb_sort($sort) 0
@@ -938 +1038 @@
 
      for {set matrixnum 1} {$matrixnum <= $::rb_matrix_num($bodnum)} {incr matrixnum} {
-         lappend temp_mat "$::rb_mult($bodnum,$matrixnum)"
+         lappend temp_mat $::rb_mult($bodnum,$matrixnum)
      }
 
@@ -944 +1044 @@
          set temp ""
          for {set atomnum 0} {$atomnum < $::::rb_coord_num($bodnum,1)} {incr atomnum} {
-                  set temp_cart_triplet "$::x($matrixnum,$atomnum) $::y($matrixnum,$atomnum) $::z($matrixnum,$atomnum)"
+                  set temp_cart_triplet "$::rb_x($bodnum,$matrixnum,$atomnum) $::rb_y($bodnum,$matrixnum,$atomnum) $::rb_z($bodnum,$matrixnum,$atomnum)"
+#                  puts "$temp_cart_triplet $atomnum"
                   lappend temp $temp_cart_triplet
                            }
@@ -958 +1059 @@
 }
 
-############################################################################################
-proc RB_View_Parameters {phase x y args} {
-   set euler     $::rb_map_euler($phase,$x,$y)
-   set positions $::rb_map_positions($phase,$x,$y)
-   set damping   $::rb_map_damping($phase,$x,$y)
-   catch {destroy .viewparam}
-   set vp .viewparam
-   toplevel $vp
-   wm title $vp "Refinement Options"
-   frame $vp.con -bd 2 -relief groove
-   frame $vp.spa -bd 2 -relief groove
-   frame $vp.refflag -bd 2 -relief groove
-   grid $vp.con -row 0 -column 0
-
-   grid $vp.spa -row 2 -column 0
-   grid $vp.refflag -row 1 -column 0
-
-   set con $vp.con
-   label $con.lbl -text "Refine: "
-   button $con.tog -text "off"
-   grid $con.lbl -row 0 -column 0
-   grid $con.tog -row 0 -column 1
-
-   grid [label $vp.spa.lbl1 -text "Supplemental Position Angles"] row 0 -column 0 -columnspan 3
-   set ::e_angle1$y [lindex [lindex $euler 3] 0]
-
-   set ::e_angle2$y [lindex [lindex $euler 4] 0]
-   set ::e_angle3$y [lindex [lindex $euler 5] 0]
-   grid [label $vp.spa.angle1l -text "Sup. Angle 1"] -row 1 -column 0
-   grid [label $vp.spa.angle2l -text "Sup. Angle 2"] -row 2 -column 0
-   grid [label $vp.spa.angle3l -text "Sup. Angle 3"] -row 3 -column 0
-   grid [entry $vp.spa.angle1 -textvariable ::e_angle1$y] -row 1 -column 1
-   grid [entry $vp.spa.angle2 -textvariable ::e_angle2$y] -row 2 -column 1
-   grid [entry $vp.spa.angle3 -textvariable ::e_angle3$y] -row 3 -column 1
-
-   set e_axis1 [lindex [lindex $euler 3] 1]
-   set e_axis2 [lindex [lindex $euler 4] 1]
-   set e_axis3 [lindex [lindex $euler 5] 1]
-
-   grid [label $vp.refflag.lbl1 -text "Refinement Flags"] -row 0 -column 0 -columnspan 3
-   grid [label $vp.refflag.x_axis -text "X-axis"] -row 1 -column 0
-   grid [label $vp.refflag.y_axis -text "Y-axis"] -row 1 -column 1
-   grid [label $vp.refflag.z_axis -text "Z-axis"] -row 1 -column 2
-   grid [label $vp.refflag.euler1 -text "Euler Angle 1"] -row 3 -column 0
-   grid [label $vp.refflag.euler2 -text "Euler Angle 2"] -row 3 -column 1
-   grid [label $vp.refflag.euler3 -text "Euler Angle 3"] -row 3 -column 2
-   grid [label $vp.refflag.sup1 -text "Sup. Angle 1"] -row 5 -column 0
-   grid [label $vp.refflag.sup2 -text "Sup. Angle 2"] -row 5 -column 1
-   grid [label $vp.refflag.sup3 -text "Sup. Angle 3"] -row 5 -column 2
-
-   for {set j 0} {$j < 9} {incr j} {
-       label $vp.refflag.$j -text [lindex $positions $j]
-   }
-   grid $vp.refflag.0 -row 2 -column 0
-   grid $vp.refflag.1 -row 2 -column 1
-   grid $vp.refflag.2 -row 2 -column 2
-   grid $vp.refflag.3 -row 4 -column 0
-   grid $vp.refflag.4 -row 4 -column 1
-   grid $vp.refflag.5 -row 4 -column 2
-   grid $vp.refflag.6 -row 6 -column 0
-   grid $vp.refflag.7 -row 6 -column 1
-   grid $vp.refflag.8 -row 6 -column 2
-
-
-
-   putontop $vp
-}
-   proc GetImportFormats {} {
+
+proc GetImportFormats {} {
     global expgui tcl_platform
     # only needs to be done once
@@ -1045 +1080 @@
 }
 
-
-
-proc RB_Load_File {location args} {
-#     eval destroy [winfo children $location]
-      destroy $location.display
-      set filelist [RB_Import_Data_Type]
-#      puts $filelist
-#     menubutton $location.but -text "File Type" -menu $location.but.menu
-#      grid [frame $location.display -bd 2 -relief groove] -row 1 -column 0
-
-#      set menuloc $location.display
-#      menu $menuloc.menu
-#      grid $menuloc.menu -row 1 -column 0
-#     foreach filetype $filelist {
-#             $location.but.menu add command -label $filetype -command "puts $filetype"
-#     }
-}
-
 proc NewBodyTypeWindow {} {
      destroy .nbt
@@ -1070 +1087 @@
      set con2 .nbt.2
      set con3 .nbt.3
-     set bodytyp [expr [llength [RigidBodyList]] + 1]
+
+     set bodnum [RB_New_RBnum]
+#     set bodnum [expr [llength [RigidBodyList]] + 1]
      pack [frame $con1 -bd 2 -relief groove] -side top -pady 10
      pack [frame $con2 -bd 2 -relief groove] -side top -expand 1 -fill both
      pack [frame $con3 -bd 2 -relief groove] -side top
-     grid [label $con1.lbl -text "New Rigid Body Type $bodytyp"] -row 0 -column 0
+     grid [label $con1.lbl -text "New Rigid Body Type $bodnum"] -row 0 -column 0
      grid [label $con1.mat -text "Number of Matricies Describing Rigid Body"] -row 1 -column 0
 
 
 
-     spinbox $con1.matnum -from 0 -to 10 -textvariable ::rb_matrix_num($bodytyp) -width 5 -command "RB_Create_Cart $bodytyp $con2"
+     spinbox $con1.matnum -from 1 -to 10 -textvariable ::rb_matrix_num($bodnum) -width 5 -command "RB_Create_Cart $bodnum $con2"
      grid $con1.matnum -row 1 -column 1 -padx 10
      grid [label $con1.atoms -text "Number of Cartesian Sites"] -row 2 -column 0
-     spinbox $con1.atomsnum -from 0 -to 1000 -textvariable ::rb_coord_num($bodytyp,1) -width 5 -command "RB_Create_Cart $bodytyp $con2"
+     spinbox $con1.atomsnum -from 3 -to 1000 -textvariable ::rb_coord_num($bodnum,1) -width 5 -command "RB_Create_Cart $bodnum $con2"
      grid $con1.atomsnum -row 2 -column 1 -padx 10
 
 
-     grid [button $con3.save -text "Save \n Rigid Body" -command "RB_Create_Save $bodytyp"] -row 0 -column 2 -padx 5 -pady 5
-     grid [button $con3.abort -text "Abort \n Rigid Body" -command "destroy .nbt; RB_Control_Panel end"] -row 0 -column 3 -padx 5 -pady 5
-
-     RB_Create_Cart $bodytyp $con2
-     bind $con1.atomsnum <Leave> "RB_Create_Cart $bodytyp $con2"
-     bind $con1.atomsnum <Return> "RB_Create_Cart $bodytyp $con2"
-     bind $con1.matnum <Leave> "RB_Create_Cart $bodytyp $con2"
-     bind $con1.matnum <Return> "RB_Create_Cart $bodytyp $con2"
+     grid [button $con3.save -text "Save \n Rigid Body" -command "RB_Create_Save $bodnum"] -row 0 -column 2 -padx 5 -pady 5
+     grid [button $con3.print -text "Save Cartesian \n Coordinates to File" -command "RB_CartesianTextFile $bodnum"] -row 0 -column 3 -padx 5
+#     $con3.print configure -status disable
+     grid [button $con3.abort -text "Abort \n Rigid Body" -command "destroy .nbt; RB_Control_Panel end"] -row 0 -column 4 -padx 5 -pady 5
+
+     RB_Create_Cart $bodnum $con2
+
+     bind $con1.atomsnum <Leave> "RB_Create_Cart $bodnum $con2"
+     bind $con1.atomsnum <Return> "RB_Create_Cart $bodnum $con2"
+     bind $con1.matnum <Leave> "RB_Create_Cart $bodnum $con2"
+     bind $con1.matnum <Return> "RB_Create_Cart $bodnum $con2"
 }
 
@@ -1099 +1121 @@
      destroy .geometry
      toplevel .geometry
+     putontop .geometry
      set geo .geometry
 
-     pack [frame $geo.con2 -bd 2 -relief groove] -side top
+
      pack [frame $geo.con -bd 2 -relief groove] -side top
      pack [frame $geo.display -bd 2 -relief groove] -side top -expand 1 -fill both
+     pack [frame $geo.con2 -bd 2 -relief groove] -side bottom
+#     pack [frame $geo.save -bd 2 -relief groove] -side bottom
 
      wm title $geo "Fix Molecular Fragment from EXP File"
@@ -1122 +1147 @@
      grid $gcon.atom -row 1 -column 1 -padx 5
      grid [button $gcon.atomchoice -text "Choose Start Atom" -command "RB_FixStartAtom $phase $gdisplay $gcon2"] -row 1 -column 2
-     grid [button $gcon2.save -text "Save Rigid Body" -width 22 -command "RB_Geom_Save"] -row 0 -column 0
+     grid [button $gcon2.save -text "Save and Map \n Rigid Body" -width 15 -command "RB_Geom_Save"] -row 0 -column 0 -padx 5
           $gcon2.save config -state disable
-     grid [button $gcon2.abort -text "Quit" -width 22 -command "destroy .geometry"] -row 1 -column 0
+     grid [button $gcon2.savec -text "Save Cartesian \n Coordinates" -width 15 -command "RB_FixFragSaveCoord"] -row 0 -column 1 -padx 5
+          $gcon2.savec config -state disable
+     grid [button $gcon2.abort -text "Abort" -width 15 -command "destroy .geometry"] -row 0 -column 2 -sticky ns -padx 5
+
+}
+
+proc RB_FixFragSaveCoord {args} {
+# number of atoms in rigid body  ::gcon_atoms
+# first atom in rigid body       ::gcon_start
+# origin list                    ::gcon_origin_list
+
+     set vector1list "X"
+     set vector2list "Y"
+
+     lappend vector1list [expr $::geom_x1 - [expr $::gcon_start -1]]
+     lappend vector1list [expr $::geom_x2 - [expr $::gcon_start -1]]
+     lappend vector2list [expr $::geom_y1 - [expr $::gcon_start -1]]
+     lappend vector2list [expr $::geom_y2 - [expr $::gcon_start -1]]
+
+     set ::gcon_origin_list ""
+     foreach item $::rb_atom_range {
+                if {$::rb_atom_origin_set($item) == 1} {
+                set temp [expr $item - [expr $::gcon_start - 1]]
+                   lappend ::gcon_origin_list $temp
+                }
+        }
+
+        set temp1 [ExtractRigidBody $::rb_phase $::gcon_atoms $::gcon_start $::gcon_origin_list $vector1list $vector2list]
+        if {[lindex $temp1 0] == {} || [lindex $temp1 1] == {} || [lindex $temp1 2] == {}} {
+   }
+
+   set coordlist ""
+   lappend coordlist [lindex $temp1 2]
+   puts $coordlist
+
+   set bodnum [RB_New_RBnum]
+   puts "body number = $bodnum"
+   set coordnum 0
+   set ::rb_damp($bodnum,1) 0
+   set ::rb_coord_num($bodnum,1) $::gcon_atoms
+
+   catch {array unset ::rb_x $bodnum,1,*}
+   catch {array unset ::rb_y $bodnum,1,*}
+   catch {array unset ::rb_z $bodnum,1,*}
+
+
+   foreach coord $coordlist {
+
+           set ::rb_x($bodnum,1,$coordnum) [lindex $coord 1]
+           set ::rb_y($bodnum,1,$coordnum) [lindex $coord 2]
+           set ::rb_z($bodnum,1,$coordnum) [lindex $coord 3]
+           incr coordnum
+   }
+
+
+   NewBodyTypeWindow
+   destroy .geometry
+#   RB_Control_Panel 0
+
 
 }
 
 proc RB_FixStartAtom {phase gdisplay gcon2 args} {
+     set ::gcon_start ""
      set possible_start [RigidStartAtoms $phase $::gcon_atoms]
+
+     if {$possible_start == ""} {
+        set ::gdisplay $gdisplay
+        #grid [label $ca.stop -text "Warning, action failed due to lack of unmapped atoms."] -row 0 -column 0
+        #grid [button $ca.cont -text "continue" -command "destroy $ca"] -row 1 -column 0
+        MyMessageBox -parent $gdisplay \
+          -message "There are not enough atoms in this phase that are not already mapped to a rigid body to use."
+        return
+     }
 
      catch {destroy .chooseatom}
@@ -1135 +1228 @@
      toplevel $ca
      wm title $ca "Choose Atom"
+
 #     puts $atomlist
      foreach {top main side lbl} [MakeScrollTable $ca] {}
@@ -1143 +1237 @@
         set label "[atominfo $phase $atom label] \($atom\)"
         button $main.$atom -text $label -command "set ::gcon_start $atom; destroy $ca"
+
         incr row
         if {$row > 5} {
@@ -1155 +1250 @@
       afterputontop
       $gcon2.save config -state normal
+      $gcon2.savec config -state normal
       RB_Atom_Fixlist $phase $gdisplay
 }
 
 proc RB_Atom_Fixlist {phase gdisplay} {
-
+#     set ::gcon_start ""
      set start_loc [lsearch $::expmap(atomlist_$phase) $::gcon_start]
      set ::rb_atom_range [lrange $::expmap(atomlist_$phase) $start_loc [expr $start_loc + $::gcon_atoms - 1]]
@@ -1280 +1376 @@
      set vector1list "X"
      set vector2list "Y"
-    
+
      lappend vector1list [expr $::geom_x1 - [expr $::gcon_start -1]]
      lappend vector1list [expr $::geom_x2 - [expr $::gcon_start -1]]
@@ -1287 +1383 @@
 
      set ::gcon_origin_list ""
-        foreach item $::rb_atom_range {
+     foreach item $::rb_atom_range {
                 if {$::rb_atom_origin_set($item) == 1} {
                 set temp [expr $item - [expr $::gcon_start - 1]]
@@ -1293 +1389 @@
                 }
         }
-#        puts "Origin list = $::gcon_origin_list"
-#        puts "vector 1 list = $vector1list"
-#        puts "vector 2 list = $vector2list"
-#        puts "number atoms = $::gcon_atoms"
-#        puts "start atom  = $::gcon_start"
+        puts "Origin list = $::gcon_origin_list"
+        puts "vector 1 list = $vector1list"
+        puts "vector 2 list = $vector2list"
+        puts "number atoms = $::gcon_atoms"
+        puts "start atom  = $::gcon_start"
 
 set temp1 [ExtractRigidBody $::rb_phase $::gcon_atoms $::gcon_start $::gcon_origin_list $vector1list $vector2list]
@@ -1311 +1407 @@
 #puts "Cartesian = $cartesian"
 
-set bodytyp [AddRigidBody 1 $cartesian]
-set ::rb_damp($bodytyp,1) 0
-set ::rb_coord_num($bodytyp,1) $::gcon_atoms
-
-MapRigidBody $::rb_phase $bodytyp $::gcon_start [lindex $temp1 0] [lindex $temp1 1]
+set bodnum [AddRigidBody 1 $cartesian]
+set ::rb_damp($bodnum,1) 0
+set ::rb_coord_num($bodnum,1) $::gcon_atoms
+
+MapRigidBody $::rb_phase $bodnum $::gcon_start [lindex $temp1 0] [lindex $temp1 1]
 
 destroy .geometry
@@ -1321 +1417 @@
 
 RB_Control_Panel 0
-}
-
-
-proc MakeRBPane {} {     ;# called to create the panel intially
-#    label $::expgui(rbFrame).l -text "RB Parameters"
-#    grid $::expgui(rbFrame).l -column 1 -row 1
-#    ResizeNotebook
-}
-
-proc DisplayRB {} {     ;# called each time the panel is raised
-    eval destroy [winfo children $::expgui(rbFrame)]
-     RB_Load_RBdata
-     RB_Control_Panel 0
-    #label $::expgui(rbFrame).l -text "RB Parameters"
-    #grid $::expgui(rbFrame).l -column 1 -row 1
-    ResizeNotebook
 }
 
@@ -1490 +1570 @@
              grid [button $con.con.clear -width 22 -text "Clear All Variables" -command {RB_Variable_Clear}] -row 5 -column 1
              grid [button $con.terminate.save -width 22 -text "Assign Variables and Save" -command RB_Var_Assign] -row 5 -column 1
-             grid [button $con.terminate.quit -width 22 -text "Quit" -command  {destroy .refcon}] -row 6 -column 1
+             grid [button $con.terminate.abort -width 22 -text "Abort" -command  {destroy .refcon}] -row 6 -column 1
 
 }
@@ -1701 +1781 @@
      }
 
-          foreach var $::rb_map_tls_var($phasenum,$bodnum,$mapnum) {
+     foreach var $::rb_map_tls_var($phasenum,$bodnum,$mapnum) {
              if {[info exists temp($var)] == "0"} {
                 set temp($var) $var
-                } else {
-                  lappend mulvarlist $var
+             } else {
+                lappend mulvarlist $var
              }
-          }
+     }
 
 
@@ -1811 +1891 @@
      return $varout
 }
-#RB_Refine_Con - sets matrix to set refinement constrols
-#RB_Var_Assign - assigns variable numbers to refinement parameters
-#RB_Var_Set    - sends variable numbers back to EXP file.
+
+#returns next unused rigid body number
+proc RB_New_RBnum {args} {
+
+     set temp [RigidBodyList]
+     for {set count 1} {[lsearch $temp $count] != -1} {incr count} {
+     }
+     return $count
+}
+
+proc RB_CartesianTextFile {bodnum args} {
+    if {$::rb_matrix_num($bodnum) > 1} {
+       MyMessageBox -message "Multiple matrices present, cannot save coordinates to file"
+       return
+    }
+    set rb_file_write [tk_getSaveFile -filetypes {{"Cartesian output" .cart} {"All files" *}}]
+    set fh [open $rb_file_write w]
+    set coordnummax $::rb_coord_num($bodnum,1)
+    for {set coord 0} {$coord < $coordnummax} {incr coord} {
+        set line [list $::rb_x($bodnum,1,$coord) $::rb_y($bodnum,1,$coord) $::rb_z($bodnum,1,$coord)]
+        puts $line
+        puts $fh $line
+    }
+    close $fh
+}
+
+############################################################################################
+proc RB_View_Parameters {phase x y args} {
+   set euler     $::rb_map_euler($phase,$x,$y)
+   set positions $::rb_map_positions($phase,$x,$y)
+   set damping   $::rb_map_damping($phase,$x,$y)
+   catch {destroy .viewparam}
+   set vp .viewparam
+   toplevel $vp
+   wm title $vp "Refinement Options"
+   frame $vp.con -bd 2 -relief groove
+   frame $vp.spa -bd 2 -relief groove
+   frame $vp.refflag -bd 2 -relief groove
+   grid $vp.con -row 0 -column 0
+
+   grid $vp.spa -row 2 -column 0
+   grid $vp.refflag -row 1 -column 0
+
+   set con $vp.con
+   label $con.lbl -text "Refine: "
+   button $con.tog -text "off"
+   grid $con.lbl -row 0 -column 0
+   grid $con.tog -row 0 -column 1
+
+   grid [label $vp.spa.lbl1 -text "Supplemental Position Angles"] row 0 -column 0 -columnspan 3
+   set ::e_angle1$y [lindex [lindex $euler 3] 0]
+
+   set ::e_angle2$y [lindex [lindex $euler 4] 0]
+   set ::e_angle3$y [lindex [lindex $euler 5] 0]
+   grid [label $vp.spa.angle1l -text "Sup. Angle 1"] -row 1 -column 0
+   grid [label $vp.spa.angle2l -text "Sup. Angle 2"] -row 2 -column 0
+   grid [label $vp.spa.angle3l -text "Sup. Angle 3"] -row 3 -column 0
+   grid [entry $vp.spa.angle1 -textvariable ::e_angle1$y] -row 1 -column 1
+   grid [entry $vp.spa.angle2 -textvariable ::e_angle2$y] -row 2 -column 1
+   grid [entry $vp.spa.angle3 -textvariable ::e_angle3$y] -row 3 -column 1
+
+   set e_axis1 [lindex [lindex $euler 3] 1]
+   set e_axis2 [lindex [lindex $euler 4] 1]
+   set e_axis3 [lindex [lindex $euler 5] 1]
+
+   grid [label $vp.refflag.lbl1 -text "Refinement Flags"] -row 0 -column 0 -columnspan 3
+   grid [label $vp.refflag.x_axis -text "X-axis"] -row 1 -column 0
+   grid [label $vp.refflag.y_axis -text "Y-axis"] -row 1 -column 1
+   grid [label $vp.refflag.z_axis -text "Z-axis"] -row 1 -column 2
+   grid [label $vp.refflag.euler1 -text "Euler Angle 1"] -row 3 -column 0
+   grid [label $vp.refflag.euler2 -text "Euler Angle 2"] -row 3 -column 1
+   grid [label $vp.refflag.euler3 -text "Euler Angle 3"] -row 3 -column 2
+   grid [label $vp.refflag.sup1 -text "Sup. Angle 1"] -row 5 -column 0
+   grid [label $vp.refflag.sup2 -text "Sup. Angle 2"] -row 5 -column 1
+   grid [label $vp.refflag.sup3 -text "Sup. Angle 3"] -row 5 -column 2
+
+   for {set j 0} {$j < 9} {incr j} {
+       label $vp.refflag.$j -text [lindex $positions $j]
+   }
+   grid $vp.refflag.0 -row 2 -column 0
+   grid $vp.refflag.1 -row 2 -column 1
+   grid $vp.refflag.2 -row 2 -column 2
+   grid $vp.refflag.3 -row 4 -column 0
+   grid $vp.refflag.4 -row 4 -column 1
+   grid $vp.refflag.5 -row 4 -column 2
+   grid $vp.refflag.6 -row 6 -column 0
+   grid $vp.refflag.7 -row 6 -column 1
+   grid $vp.refflag.8 -row 6 -column 2
+
+
+
+ }
+