Forgot to cvs rm it.

(Portage version: 2.1_pre4-r1)

2 files changed, 5 insertions, 571 deletions

diff --git a/sci-chemistry/maid/ChangeLog b/sci-chemistry/maid/ChangeLog
index 96f5dc439cf4..e8f1fece7dd9 100644
--- a/sci-chemistry/maid/ChangeLog
+++ b/sci-chemistry/maid/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/maid
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/ChangeLog,v 1.4 2006/02/23 18:56:49 spyderous Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/ChangeLog,v 1.5 2006/02/23 18:58:09 spyderous Exp $
+
+  23 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>;
+  -files/fix-compilation.patch:
+  Forgot to cvs rm it.
 
   23 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>; maid-20011112.ebuild:
   (#123634) Push big patch to mirrors.
diff --git a/sci-chemistry/maid/files/fix-compilation.patch b/sci-chemistry/maid/files/fix-compilation.patch
deleted file mode 100644
index da280e4436f5..000000000000
--- a/sci-chemistry/maid/files/fix-compilation.patch
+++ /dev/null
@@ -1,570 +0,0 @@
-diff -ur glmaid_dist.orig/drawwindow.c++ glmaid_dist/drawwindow.c++
---- glmaid_dist.orig/drawwindow.c++	2001-11-12 05:35:50.000000000 -0800
-+++ glmaid_dist/drawwindow.c++	2005-12-15 08:09:55.000000000 -0800
-@@ -659,7 +659,7 @@
-         { "OK",     fuse_ok_pushed,    NULL         },
-         { "PICK AGAIN",    pickagain_pushed ,NULL         },
-         { "QUIT", fuse_cancel_pushed,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-@@ -737,7 +737,7 @@
-         { "OK",     assign_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", assignclose_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-@@ -805,7 +805,7 @@
-         { "OK",     remove_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", removecancel_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-diff -ur glmaid_dist.orig/fit.c++ glmaid_dist/fit.c++
---- glmaid_dist.orig/fit.c++	2001-11-12 05:35:50.000000000 -0800
-+++ glmaid_dist/fit.c++	2005-12-15 08:15:43.000000000 -0800
-@@ -305,7 +305,7 @@
-         { "OK",     inputfit_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", close_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-@@ -430,7 +430,7 @@
-       fit[ii].val2= -1;
-    }
-    savefit(); //save the val2 segment unassignments
--#endif;          
-+#endif
- #if 0
-      strcpy(ranknum,"rank1fit");
-      readset("set1",fitset);
-@@ -710,16 +710,16 @@
-    buildmenu=XmVaCreateSimplePulldownMenu (menubar, "build_menu", 3, build_cb,
-         XmVaPUSHBUTTON,traceonoff,'T', NULL, NULL,  // button_0
-         XmVaPUSHBUTTON,extend,'T', NULL, NULL,  // button_1
--        XmVaPUSHBUTTON,fusepicks,'FP', NULL, NULL,  // button_2
-+        XmVaPUSHBUTTON,fusepicks,"FP", NULL, NULL,  // button_2
-         XmVaPUSHBUTTON,recallfit,'F', NULL, NULL,  // button_3
-         XmVaPUSHBUTTON,recallbackupfit,'F', NULL, NULL,  // button_4
--        XmVaCHECKBUTTON,drawfit,'DF', NULL, NULL,  // button_5
--        XmVaCHECKBUTTON,pickfit,'DF', NULL, NULL,  // button_6
--        XmVaPUSHBUTTON,inputfit,'DF', NULL, NULL,  // button_7
--        XmVaPUSHBUTTON,drawrankfit,'DR', NULL, NULL,  // button_8
--        XmVaPUSHBUTTON,drawrankset,'DR', NULL, NULL,  // button_9
--        XmVaPUSHBUTTON,fittopdb,'DR', NULL, NULL,  // button_10
--        XmVaPUSHBUTTON,deletefit,'DR', NULL, NULL,  // button_11
-+        XmVaCHECKBUTTON,drawfit,"DF", NULL, NULL,  // button_5
-+        XmVaCHECKBUTTON,pickfit,"DF", NULL, NULL,  // button_6
-+        XmVaPUSHBUTTON,inputfit,"DF", NULL, NULL,  // button_7
-+        XmVaPUSHBUTTON,drawrankfit,"DR", NULL, NULL,  // button_8
-+        XmVaPUSHBUTTON,drawrankset,"DR", NULL, NULL,  // button_9
-+        XmVaPUSHBUTTON,fittopdb,"DR", NULL, NULL,  // button_10
-+        XmVaPUSHBUTTON,deletefit,"DR", NULL, NULL,  // button_11
-         NULL);
- #if 1
-     XmStringFree (traceonoff);   
-@@ -774,12 +774,12 @@
-         XmVaPUSHBUTTON,tordyncen,'M', NULL, NULL,  // button_3
-         XmVaCASCADEBUTTON,addcresidue,'W',   // button_4
-         XmVaCASCADEBUTTON,addnresidue,'W',   // button_5
--        XmVaPUSHBUTTON,remcresidue,'RC', NULL, NULL,  // button_6
--        XmVaPUSHBUTTON,remnresidue,'RN', NULL, NULL,  // button_7
--        XmVaPUSHBUTTON,extendpickcterm,'RN', NULL, NULL,  // button_8
--        XmVaCHECKBUTTON,drawgeo,'DF', NULL, NULL,  // button_9
--        XmVaPUSHBUTTON,savepickfit,'DF', NULL, NULL,  // button_10
--        XmVaPUSHBUTTON,drawrotomer,'DR', NULL, NULL,  // button_11
-+        XmVaPUSHBUTTON,remcresidue,"RC", NULL, NULL,  // button_6
-+        XmVaPUSHBUTTON,remnresidue,"RN", NULL, NULL,  // button_7
-+        XmVaPUSHBUTTON,extendpickcterm,"RN", NULL, NULL,  // button_8
-+        XmVaCHECKBUTTON,drawgeo,"DF", NULL, NULL,  // button_9
-+        XmVaPUSHBUTTON,savepickfit,"DF", NULL, NULL,  // button_10
-+        XmVaPUSHBUTTON,drawrotomer,"DR", NULL, NULL,  // button_11
-         NULL);
- 
-   addcpullright = XmVaCreateSimplePulldownMenu (fitmenu,
-diff -ur glmaid_dist.orig/global.h glmaid_dist/global.h
---- glmaid_dist.orig/global.h	2001-11-12 05:35:51.000000000 -0800
-+++ glmaid_dist/global.h	2005-12-15 08:09:55.000000000 -0800
-@@ -6,7 +6,7 @@
- #include  <assert.h>
- #include <stdlib.h>
- #include <stdio.h>
--//#include <iostream.h>
-+//#include <iostream>
- //#include <iomanip.h>
- #include <time.h>
- #include <math.h>
-diff -ur glmaid_dist.orig/mainscreen.c++ glmaid_dist/mainscreen.c++
---- glmaid_dist.orig/mainscreen.c++	2001-11-12 05:35:49.000000000 -0800
-+++ glmaid_dist/mainscreen.c++	2005-12-15 08:09:55.000000000 -0800
-@@ -1,7 +1,7 @@
- // mainscreen.c++  - Screen version  (most general) of maid
- // the motif organizatrion was originally adapted from program levitt/motifman/ch04/dynapix.c
- 
--#include <CC/iostream.h>
-+#include <iostream>
- #include "Xgl.h"
- #include "drawwindow.h"  // also calls global.h
- #include "trace.h"
-@@ -53,7 +53,7 @@
- int splitscreen =1; // if = 1 then use standard splitscreen stereo, 
- //int splitscreen =0; // = 0 use wholescreen - also set geo.linewidth = 4 below
- 
--void main(int argc, char *argv[]) {
-+int main(int argc, char *argv[]) {
-    
-     Arg resources[20];	
-     int n;
-@@ -209,5 +209,7 @@
- #endif
- #endif
-     XtAppMainLoop(sc.appctx);
-+
-+	return 0;
- }
- 
-diff -ur glmaid_dist.orig/makefile_graphics glmaid_dist/makefile_graphics
---- glmaid_dist.orig/makefile_graphics	2001-11-12 05:35:52.000000000 -0800
-+++ glmaid_dist/makefile_graphics	2005-12-15 08:16:00.000000000 -0800
-@@ -36,109 +36,111 @@
- COMBINE = combine.h
- SELENOMET = selenomet.h
- 
--CC = CC -c -O
-+Cgeneric = gcc
-+Clink = $(Cgeneric)
-+Copt = $(Cgeneric) -c -O
- 
- 
- auto:  $(OBJ) 
--	CC $(OBJ) -lGLw -lGL -lGLU -lXm -lXt -lX11 -lm  -o maid
-+	$(Clink) $(OBJ) -lGLw -lGL -lGLU -lXm -lXt -lX11 -lm  -o maid
- 
- mainscreen.o: mainscreen.c++  $(DRAWWIND) $(MATH)  $(CONTROL)  $(PEPTIDE) $(TORDYN) $(TRACE) $(ASSIGNSEQ) $(EXTENDFIT) $(EDITBONES)
--	$(CC) mainscreen.c++
-+	$(Copt) mainscreen.c++
- 
- symmate.o:  symmate.c++   $(GLOBAL) $(PEPTIDE) $(TRACE) $(MATH) $(PDBTOLEV) $(SYMMATE) $(COMBINE)
--	$(CC) symmate.c++
-+	$(Copt) symmate.c++
- 
- selenomet.o:  selenomet.c++   $(GLOBAL) $(MATH) $(SELENOMET)
--	$(CC) selenomet.c++
-+	$(Copt) selenomet.c++
- 
- combine.o:  combine.c++   $(GLOBAL) $(PEPTIDE) $(TRACE) $(MATH) $(COMBINE) $(SYMMATE) $(FITTOPDB)
--	$(CC) combine.c++
-+	$(Copt) combine.c++
- 
- control.o:  control.c++   $(GLOBAL) $(PEPTIDE) $(CONTROL) $(TORDYN) $(ASSIGNSEQ) $(PDBTOLEV) $(TRACE)  $(RANKSIDE) $(BONE)	
--	$(CC) control.c++
-+	$(Copt) control.c++
- 
- extend2.o:  extend2.c++  $(MATH) $(TRACE)  $(GLOBAL) $(EXTENDFIT) $(PEPTIDE)  $(BONE) $(EXTEND2) $(TORDYN) 	
--	$(CC) extend2.c++
-+	$(Copt) extend2.c++
- 
- checkfit.o:  checkfit.c++  $(MATH) $(TRACE)  $(GLOBAL) $(PEPTIDE) $(TORDYN) $(CHECKFIT) $(EDITBONES) $(BONE)
--	$(CC) checkfit.c++
-+	$(Copt) checkfit.c++
- 
- refine.o:  refine.c++  $(MATH) $(TRACE)  $(GLOBAL) $(REFINE) $(PEPTIDE) $(TORDYN)
--	$(CC) refine.c++
-+	$(Copt) refine.c++
- 
- rankside.o:  rankside.c++  $(PDBTOLEV) $(MATH) $(TRACE) $(RANKSIDE) $(GLOBAL) $(TORDYN) $(MODEL) $(PEPTIDE) $(EDITBONES) 
--	$(CC) rankside.c++
-+	$(Copt) rankside.c++
- 
- extendfit.o: extendfit.c++  $(DRAWWIND) $(SYMMATE) $(REFINE) $(MATH) $(BONE) $(PEPTIDE) $(TRACE) $(TORDYN) $(EXTENDFIT) $(FITTOPDB) $(EDITBONES) $(RANKSIDE) $(ASSIGNSEQ) 
--	$(CC) extendfit.c++
-+	$(Copt) extendfit.c++
- 
- editbones.o: editbones.c++  $(EDITBONES) $(DRAWWIND) $(MATH) $(BONE) $(PEPTIDE) $(TRACE) $(TORDYN) $(EXTENDFIT)
--	$(CC) editbones.c++
-+	$(Copt) editbones.c++
- 
- fittopdb.o: fittopdb.c++   $(DRAWWIND) $(PEPTIDE) $(FITTOPDB) $(PDBTOLEV)
--	$(CC) fittopdb.c++
-+	$(Copt) fittopdb.c++
- 
- tordyn.o: tordyn.c++  $(TORDYN)  $(DRAWWIND) $(PEPTIDE) $(MENU) $(TRACE) $(ASSIGNSEQ)  $(RUNTORDYN) $(EDITBONES) $(EXTENDFIT) $(REFINE)
--	$(CC) tordyn.c++
-+	$(Copt) tordyn.c++
- 
- runtordynnew.o: runtordynnew.c++   $(TRACE) $(TORDYN) $(RUNTORDYN) $(PEPTIDE) $(EDITBONES) $(REFINE) 
--	$(CC) runtordynnew.c++
-+	$(Copt) runtordynnew.c++
- 
- assignseq.o: assignseq.c++   $(PDBTOLEV) $(TRACE) $(ASSIGNSEQ) $(GLOBAL) $(TORDYN) $(MODEL) $(PEPTIDE) $(RANKSIDE)  $(EDITBONES) $(SYMMATE)
--	$(CC) assignseq.c++
-+	$(Copt) assignseq.c++
- 
- peptide.o: peptide.c++  $(DRAWWIND) $(MATH) $(PEPTIDE)
--	$(CC) peptide.c++
-+	$(Copt) peptide.c++
- 
- initialize.o: initialize.c++ $(DRAWWIND) $(PEPTIDE) $(TORDYN) $(BONE) $(TRACE)
--	$(CC) initialize.c++
-+	$(Copt) initialize.c++
- 
- bone.o: bone.c++  $(DRAWWIND) $(MATH) $(BONE) 
--	$(CC) bone.c++
-+	$(Copt) bone.c++
- 
- trace.o: trace.c++   $(DRAWWIND) $(MATH) $(BONE) $(PEPTIDE) $(TRACE) $(TORDYN) $(EXTENDFIT)  $(CHECKFIT) $(FITTOPDB)
--	$(CC) trace.c++
-+	$(Copt) trace.c++
- 
- pdbtolev.o: pdbtolev.c++  $(INITIALIZE) $(PDBTOLEV) $(GLOBAL) $(MENU) $(DRAWWIND) $(PEPTIDE) $(FITTOPDB)
--	$(CC) pdbtolev.c++
-+	$(Copt) pdbtolev.c++
- 
- math.o: math.c++  $(MATH) $(PEPTIDE) $(TRACE)
--	$(CC) math.c++
-+	$(Copt) math.c++
- 
- global.o: global.c++  $(GLOBAL)
--	$(CC) global.c++
-+	$(Copt) global.c++
- 
- drawwindow.o: drawwindow.c++  $(MENU) $(DRAWWIND)  $(CUBE) $(PEPTIDE)  $(ASSIGNSEQ) $(FIT) $(EXTENDFIT)  $(EDITBONES)
--	$(CC) drawwindow.c++
-+	$(Copt) drawwindow.c++
- 
- 
- mapmenu.o: mapmenu.c++ $(MAPMENU) $(DRAWWIND) $(MENU) $(CORE) $(COMBINE) $(PEPTIDE) $(EXTENDFIT) $(CONTROL)  $(EDITBONES) $(INITIALIZE)
--	$(CC) mapmenu.c++
-+	$(Copt) mapmenu.c++
- 
- 
- menu.o: menu.c++ $(MENU) $(DRAWWIND) $(PDBTOLEV) $(MATH) $(MARCH) $(PEPTIDE) $(TRACE) $(INITIALIZE)
--	$(CC) menu.c++
-+	$(Copt) menu.c++
- 
- pdbmenu.o: pdbmenu.c++ $(PDBMENU) $(DRAWWIND) $(MENU) $(FITTOPDB) $(COMBINE) $(PEPTIDE)
--	$(CC) pdbmenu.c++
-+	$(Copt) pdbmenu.c++
- 
- sphere.o: sphere.c++ $(DRAWWIND) $(MATH) $(SPHERE)
--	$(CC) sphere.c++
-+	$(Copt) sphere.c++
- 
- cube.o: cube.c++  $(CUBE) $(DRAWWIND) 
--	$(CC) cube.c++
-+	$(Copt) cube.c++
- 
- model.o: model.c++ $(MODEL) $(DRAWWIND) $(PDBTOLEV) $(MATH)
--	$(CC) model.c++
-+	$(Copt) model.c++
- 
- fit.o: fit.c++ testfit.inc $(DRAWWIND) $(RANKSIDE) $(TRACE) $(FIT) $(MENU) $(BONE) $(TORDYN)  $(PEPTIDE) $(ASSIGNSEQ) $(FITTOPDB) $(EXTENDFIT) $(RANKSIDE)
--	$(CC) fit.c++
-+	$(Copt) fit.c++
- 
- contour.o: contour.c++ $(CONTOUR) $(DRAWWIND) $(TRACE) 
--	$(CC) contour.c++
-+	$(Copt) contour.c++
- 
- initializescreen.o: initializescreen.c++  $(INITIALIZESCREEN) $(DRAWWIND) $(PEPTIDE) $(TORDYN) $(BONE)
--	$(CC) initializescreen.c++
--
--
-+	$(Copt) initializescreen.c++
- 
-+clean:
-+	rm -f *.o maid
-diff -ur glmaid_dist.orig/mapmenu.c++ glmaid_dist/mapmenu.c++
---- glmaid_dist.orig/mapmenu.c++	2001-11-12 05:35:50.000000000 -0800
-+++ glmaid_dist/mapmenu.c++	2005-12-15 08:09:55.000000000 -0800
-@@ -188,7 +188,7 @@
-         { "OK",     inputfitnum_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", close_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-@@ -241,7 +241,7 @@
-         { "OK",     inputbone_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", close_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-@@ -806,7 +806,7 @@
-              XmVaCASCADEBUTTON,contlevel,NULL,
-              XmVaCASCADEBUTTON,boneminset,NULL,
-              NULL);
--   for(i=1;i<NMAPS;i++) // Turn off sensitivitivity  - look pale
-+   for(int i=1;i<NMAPS;i++) // Turn off sensitivitivity  - look pale
-        XtSetSensitive(sc.mappullright[i],0);
- 
-    colorpullright[1]=XmVaCreateSimplePulldownMenu (sc.mappullright[1],
-@@ -1156,11 +1156,11 @@
-             XtVaSetValues (widget, XmNset,False, NULL);
-   if (widget = XtNameToWidget (mapmenu,"button_9")) //DEFAULT:  Turn off check box for highlight bone point on/off button
-             XtVaSetValues (widget, XmNset,False, NULL);
--    for(i=0;i<=6;i++){
-+    for(int i=0;i<=6;i++){
-        XmStringFree (radius[i]);
-        XmStringFree (minden[i]);
-     }
--    for(i=0;i<=9;i++){
-+    for(int i=0;i<=9;i++){
-        XmStringFree (colorv[i]);
-        XmStringFree (level[i]);
-     }
-@@ -1175,7 +1175,7 @@
-     XmStringFree(editboneonoff);
-     XmStringFree(inputbonept);
-     XmStringFree(inputfitnum);
--    for(i=1;i<NMAPS;i++)
-+    for(int i=1;i<NMAPS;i++)
-        XmStringFree (xmpdb[i]);
-  }   
-     
-diff -ur glmaid_dist.orig/menu.c++ glmaid_dist/menu.c++
---- glmaid_dist.orig/menu.c++	2001-11-12 05:35:50.000000000 -0800
-+++ glmaid_dist/menu.c++	2005-12-15 08:09:55.000000000 -0800
-@@ -1,5 +1,5 @@
- // This is primarily the menus associated with FILE pulldown menu
--#include <CC/iostream.h>
-+#include <iostream>
- #include <stdlib.h>
- #include <stdio.h>
- #include <math.h>
-@@ -85,7 +85,7 @@
-         { "OK",     new_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", close_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-@@ -159,7 +159,7 @@
-         { "OK",     old_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", close_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-@@ -211,7 +211,7 @@
- 
- 
- /* The "ok" button was pushed or the user pressed Return */
--static void old_ok_pushed(Widget w,XtPointer  client_data,XtPointer  call_data)
-+extern void old_ok_pushed(Widget w,XtPointer  client_data,XtPointer  call_data)
- {
-     char* text[5];
-     char text0[100];
-@@ -219,14 +219,14 @@
-         text[i] =   XmTextFieldGetString (ss.w[i]);
-       
-     strcpy(text0,text[0]);
--    for( i = 0;i< ss.num;i++)
-+    for(int i = 0;i< ss.num;i++)
-       XtFree (text[i]);
-     strcat(text0,".maid");
-     strcpy(maidfile.name,text0);
- //    readmaidfile(maidfile,map,core);
-     readmaidfile(maidfile,map,bone);
- printf(" npdbfile = %d\n",maidfile.npdb);
--for(i=1;i<=maidfile.npdb;i++)
-+for(int i=1;i<=maidfile.npdb;i++)
-    printf("pdbfilename%d = %s\n",i,maidfile.pdb[i].name);
-     Widget shell = (Widget) client_data;
-     XtDestroyWidget (shell);
-@@ -240,7 +240,7 @@
- }
- 
- /* The "ok" button was pushed or the user pressed Return */
--static void new_ok_pushed(Widget w,XtPointer  client_data,XtPointer  call_data)
-+extern void new_ok_pushed(Widget w,XtPointer  client_data,XtPointer  call_data)
- {
-     char* text[5];
-     char text0[100],ich[10];
-@@ -277,7 +277,7 @@
-     XtDestroyWidget (shell);
- printf ("Name = %s pdbfile = %s mapfile = %s\n",
-       maidfile.name,maidfile.pdb[1].name,text[2]);
--    for( i = 0;i< ss.num;i++)
-+    for(int i = 0;i< ss.num;i++)
-       XtFree (text[i]);
-     maidfile.start=0;  // This starts routine (as set by RUN command)
- }
-@@ -654,7 +654,7 @@
-     for(int i = 0;i< ss.num;i++)
-         text[i] =   XmTextFieldGetString (ss.w[i]);      
-     strcpy(text0,text[0]);
--    for( i = 0;i< ss.num;i++)
-+    for(int i = 0;i< ss.num;i++)
-       XtFree (text[i]);
-     
-     if( (fp=fopen(text[0],"r") ) ==NULL) { // check if file exists
-@@ -694,7 +694,7 @@
-         { "OK",     pdb_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", close_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-@@ -749,7 +749,7 @@
-     for(int i = 0;i< ss.num;i++)
-         text[i] =   XmTextFieldGetString (ss.w[i]);      
-     strcpy(text0,text[0]);
--    for( i = 0;i< ss.num;i++)
-+    for(int i = 0;i< ss.num;i++)
-       XtFree (text[i]);
- 
-     if( (fp=fopen(text0,"r") ) ==NULL) { // check if file exists
-@@ -788,7 +788,7 @@
-         { "OK",     map_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", close_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-diff -ur glmaid_dist.orig/pdbmenu.c++ glmaid_dist/pdbmenu.c++
---- glmaid_dist.orig/pdbmenu.c++	2001-11-12 05:35:50.000000000 -0800
-+++ glmaid_dist/pdbmenu.c++	2005-12-15 08:09:55.000000000 -0800
-@@ -755,7 +755,7 @@
-              XmNradioBehavior, True,     /* RowColumn resources to enforce */
-              XmNradioAlwaysOne, True,    /* radio behavior in Menu */
-              NULL);   
--    for(i=1;i<MAXPDB;i++){ // set default values for main color = yellow     
-+    for(int i=1;i<MAXPDB;i++){ // set default values for main color = yellow     
-         if (widget = XtNameToWidget (colorpullright[i], "button_3")) 
-                 XtVaSetValues (widget, XmNset,True, NULL);
-     }
-@@ -895,11 +895,11 @@
-              XmNradioBehavior, True,     /* RowColumn resources to enforce */
-              XmNradioAlwaysOne, True,    /* radio behavior in Menu */
-              NULL);   
--    for(i=1;i<MAXPDB;i++){ // set default values for side color = light blue     
-+    for(int i=1;i<MAXPDB;i++){ // set default values for side color = light blue     
-         if (widget = XtNameToWidget (colorpullright[i], "button_2")) 
-                 XtVaSetValues (widget, XmNset,True, NULL);
-     }
--    for(i=1;i<MAXPDB;i++){ // Turn off sensitivitivity  - look pale
-+    for(int i=1;i<MAXPDB;i++){ // Turn off sensitivitivity  - look pale
-        XtSetSensitive(sc.pullright[i],0);
-     }
-    if (widget = XtNameToWidget (radpullright, "button_2"))
-@@ -917,11 +917,11 @@
-     XmStringFree (refineside);
-     XmStringFree (refineallside);
-     XmStringFree (rotatepdb);
--    for(i=1;i<MAXPDB;i++)
-+    for(int i=1;i<MAXPDB;i++)
-        XmStringFree (xmpdb[i]);
--    for(i=0;i<=6;i++)
-+    for(int i=0;i<=6;i++)
-        XmStringFree (radius[i]);
--    for(i=0;i<=9;i++)
-+    for(int i=0;i<=9;i++)
-        XmStringFree (colorv[i]);
-     XmStringFree( setradius); 
-     XmStringFree(maincolor);
-@@ -976,7 +976,7 @@
-        pdbn = 1;
- printf("segn = %d  pdbn = %d\n",segn,pdbn);
-  
--    for(i=1;i<=maidfile.pdb[pdbn].resdat[segn+1][0][0];i++) { 
-+    for(int i=1;i<=maidfile.pdb[pdbn].resdat[segn+1][0][0];i++) { 
-        if(strcmp(text[0],maidfile.pdb[pdbn].resnumch[segn][i])== 0){
-           resn =i;
-           goto quiti;
-@@ -995,7 +995,7 @@
-          errormessage(toplevel,"You are near allowed limit of pdb labels.. 'Delete Label' and continue");
-     maidfile.pdb[pdbn].pickres[pnum].seg = segn;
-     maidfile.pdb[pdbn].pickres[pnum].num = resn;
--    for(i=0;i<=2;i++)
-+    for(int i=0;i<=2;i++)
-          sc.centerpos[i] = maidfile.pdb[pdbn].mainch[segn][resn][1][i];
-     if(sc.pdbwindow==1){ // Then window about centerpos
-           findpdbwind();
-@@ -1004,7 +1004,7 @@
-     }
-     else if (sc.pdbwindow !=1)
-            sc.windowselect = -1;
--    for(i=1;i<= maidfile.nden;i++){ // contour about input fit
-+    for(int i=1;i<= maidfile.nden;i++){ // contour about input fit
-             if(map[i].contonoff ==1)
-                 contourmap(map[i],sc.centerpos);
-             sc.drawcontour = 1; // Turn on drawing of contour
-@@ -1024,7 +1024,7 @@
-         { "OK",     center_ok_pushed,     NULL          },
-         { "Clear",  clear_pushed,  NULL          },
-         { "Cancel", close_dialog,  NULL          },
--        { "Help",   help,          "Help Button" },
-+        { "Help",   help,          (void *) "Help Button" },
-     };
-     /* Create a TemplateDialog that will contain the control area
-      * and the action area buttons for the dialog
-diff -ur glmaid_dist.orig/selenomet.c++ glmaid_dist/selenomet.c++
---- glmaid_dist.orig/selenomet.c++	2001-11-12 05:35:50.000000000 -0800
-+++ glmaid_dist/selenomet.c++	2005-12-15 08:18:11.000000000 -0800
-@@ -75,7 +75,7 @@
-         for (line_col = 0; line_col < LINE_WIDTH; line_col++) {
- 
-                 digit = op_line[line_col];
--                if (digit == NULL || digit == '\n') {
-+                if (digit == 0 || digit == '\n') {
-                         break;
-                 }
-                 else if(digit == ',') {
-diff -ur glmaid_dist.orig/tordyn.c++ glmaid_dist/tordyn.c++
---- glmaid_dist.orig/tordyn.c++	2001-11-12 05:35:49.000000000 -0800
-+++ glmaid_dist/tordyn.c++	2005-12-15 08:13:32.000000000 -0800
-@@ -2748,7 +2748,7 @@
- #if 1
-            if(geo.quit==1){
-                if(verbose>=2)// 30nov00 - do not print this line
--                   printf(" For quitcond >2: NOTE NOTE!!  geo.quit = 1 after tordyn (near boundary??) - quitting\n");
-+                   printf(" For quitcond >2: NOTE NOTE!!  geo.quit = 1 after tordyn (near boundary\?\?) - quitting\n");
-                goto quit1;
-            }
-            if(checkanglimit(tordata) ==1){
-@@ -2824,7 +2824,7 @@
-            runtordyn(den1,geo,tordata,tordata2);
- #if 1
-            if(geo.quit==1){
--               printf("NOTE  NOTE!!:  geo.quit = 1 after tordyn at 2 (near boundary??) - quitting\n");
-+               printf("NOTE  NOTE!!:  geo.quit = 1 after tordyn at 2 (near boundary\?\?) - quitting\n");
-                goto quitwhile;
-            }
-            if(checkanglimit(tordata) ==1){
-diff -ur glmaid_dist.orig/Xgl.h glmaid_dist/Xgl.h
---- glmaid_dist.orig/Xgl.h	2001-11-12 05:35:51.000000000 -0800
-+++ glmaid_dist/Xgl.h	2005-12-15 08:09:55.000000000 -0800
-@@ -11,7 +11,7 @@
- #include <Xm/RowColumn.h>
- #include <Xm/MessageB.h>
- #include <Xm/CascadeBG.h>
--#include <X11/GLw/GLwMDrawA.h>
-+#include <GL/GLwMDrawA.h>
- #include <X11/keysym.h>
- #include <X11/Xutil.h>
- #include <GL/glx.h>