--- makedef.orig	1969-12-31 16:00:00.000000000 -0800
+++ makedef	2005-05-28 09:44:47.000000000 -0700
@@ -0,0 +1,60 @@
+ TIFFDIR = @PREFIX@/lib
+ MESADIR = 
+ JPEGDIR = @PREFIX@/lib
+
+ PNGDIR = @PREFIX@/lib
+ ZLIBDIR = @PREFIX@/lib
+
+# If you configured any of the above three image formats, uncomment
+# the following four lines, and delete the non-relevant parts if
+# necessary, i. e. if you did not configure all three formats.
+#
+ IMGDEF  = -DTIFF_SUPPORT -DJPEG_SUPPORT -DPNG_SUPPORT
+ IMGINCL = -I$(TIFFDIR) -I$(JPEGDIR) -I$(PNGDIR) -I$(ZLIBDIR)
+ IMGLIB  = $(TIFFDIR)/libtiff.dylib $(JPEGDIR)/libjpeg.dylib \
+           $(PNGDIR)/libpng.dylib $(ZLIBDIR)/libz.dylib
+
+# Some systems do not have the float versions of various math functions,
+# uncomment the following lines if this is the case
+
+  MISSFUNC = -Dsqrtf=sqrt -Dexpf=exp -Dlogf=log \
+             -Dsinf=sin -Dcosf=cos  \
+             -Dfabsf=fabs  -DMAXINT=INT_MAX
+	     
+	     # -Dceilf=ceil
+
+CPP = /usr/bin/cpp
+
+MCPPFLAGS =  -DMAXINT=INT_MAX -I@PREFIX@/include -I$(TOP)
+
+CC = @CC@
+
+MCFLAGS = -O -Wall
+
+RANLIB = /usr/bin/ranlib
+
+WAIT = /bin/sleep 2
+
+SHELL = /bin/sh
+
+SGDEVDIR = ogl x11 no pov rib vrml1 vrml2 ps fm
+
+SGDEVDEF = -DSG_DEV_OGL -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4
+
+PUDEVDIR = motif tty
+
+PUDEVDEF = -DPU_DEV_MOTIF -DPU_DEV_TTY
+
+IODEVDIR = motx11 motogl ttyno
+
+IODEVDEF = -DIO_DEV_MOTIF_X11 -DIO_DEV_MOTIF_OGL -DIO_DEV_TTY_NO
+
+
+MOTIFDEF = -DFUNCPROTO
+
+SYSLIB = -L/usr/lib -L@PREFIX@/lib \
+         -lX11 -lXm -lGLU -lGL /System/Library/Frameworks/OpenGL.framework/Libraries/libGL.dylib @PREFIX@/lib/libGLw.dylib \
+         -lXmu -lXt -lXp -lXpm -lX11 -lXext -lSM -lICE -lm -lc -lmx
+
+TOOLSDIR = $(TOP)/tools
+SGDIR    = $(TOP)/sg
--- molmol.orig	2003-01-20 17:44:58.000000000 -0800
+++ molmol	2005-05-28 09:44:48.000000000 -0700
@@ -1,9 +1,9 @@
-#!/bin/ksh
+#!/bin/zsh -f
 #
 # startup script for MOLMOL
 #
 
-MOLMOLHOME=/opt/group/MOLMOL
+MOLMOLHOME=@PREFIX@/share/molmol;MOLMOLDEV="Motif/OpenGL"
 export MOLMOLHOME
 export MOLMOLDEV
 
@@ -11,55 +11,8 @@
 osrel=`uname -r`
 osmaj=`echo $osrel | awk -F. '{print $1}'`
 osmin=`echo $osrel | awk -F. '{print $2}'`
-localdev=
-glxdev=
-
-if [ $ostype = "IRIX" -o $ostype = "IRIX64" ]; then
-  if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then
-    arch=sgi6
-    localdev=Motif/OpenGL
-    glxdev=Motif/OpenGL
-  elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then
-    arch=sgi5
-    localdev=Motif/OpenGL
-    glxdev=Motif/OpenGL
-  else
-    arch=sgi4
-    localdev=Motif/GL
-  fi
-  MONITOR=72HZ; export MONITOR
-elif [ $ostype = "AIX" ]; then
-  arch=aix
-  localdev=Motif/OpenGL
-elif [ $ostype = "HP-UX" ]; then
-  arch=hp
-  localdev=Motif/OpenGL
-  glxdev=Motif/OpenGL
-elif [ $ostype = "OSF1" ]; then
-  arch=dec
-  localdev=Motif/OpenGL
-elif [ $ostype = "Linux" ]; then
-  arch=lnx
-  localdev=Motif/OpenGL
-elif [ $ostype = "SunOS" ]; then
-  if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then
-    arch=sol
-    localdev=Motif/OpenGL
-  else
-    arch=sun
-  fi
-else
-  arch=unknown
-fi
-
-if [ $ostype = "SunOS" ]; then
-  xdpy=/usr/openwin/bin/xdpyinfo
-elif [ $ostype = "HP-UX" ]; then
-  xdpy=/usr/contrib/bin/X11/xdpyinfo
-else
-  xdpy=/usr/bin/X11/xdpyinfo
-fi
-
+localdev=Motif/OpenGL
+glxdev=Motif/OpenGL
 printUsage () {
   echo "Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files"
   echo ""
@@ -209,7 +162,7 @@
 fi
 
 if [ "$input" = "-" -o -n "$nograph" ]; then
-  $MOLMOLHOME/molmol.$arch $xopt
+    echo "LineBond solid 1  "  >>| $startmacro ; @PREFIX@/share/molmol/src/main/molmol $xopt
 else
-  $MOLMOLHOME/molmol.$arch $xopt < /dev/null
+    echo "LineBond solid 1  "  >>| $startmacro ; @PREFIX@/share/molmol/src/main/molmol $xopt
 fi
--- src/iodev/IODev.c.orig	2001-05-27 14:03:30.000000000 -0700
+++ src/iodev/IODev.c	2005-05-28 11:03:09.000000000 -0700
@@ -44,7 +44,6 @@
 #endif
 #ifdef IO_DEV_MOTIF_OGL
 extern void IOMotifOGLSetDev(void);
-extern void IOMotifOGLDSetDev(void);
 #endif
 #ifdef IO_DEV_MOTIF_XGL
 extern void IOMotifXGLSetDev(void);
@@ -76,7 +75,6 @@
 #endif
 #ifdef IO_DEV_MOTIF_OGL
   {"Motif/OpenGL", IOMotifOGLSetDev},
-  {"Motif/OpenGLD", IOMotifOGLDSetDev},
 #endif
 #ifdef IO_DEV_MOTIF_XGL
   {"Motif/XGL", IOMotifXGLSetDev},
--- src/motogl/MotOGL.c.orig	2000-05-29 09:31:51.000000000 -0700
+++ src/motogl/MotOGL.c	2005-05-28 09:44:50.000000000 -0700
@@ -31,7 +31,7 @@
 #include <Xm/XmStrDefs.h>
 
 #define BOOL MOTIF_BOOL  /* hack to avoid naming conflict */
-#include <X11/GLw/GLwMDrawA.h>
+#include <GL/GLwMDrawA.h>
 #undef BOOL
 
 #include <sg.h>
--- src/os/GFile.c.orig	2001-06-17 11:59:17.000000000 -0700
+++ src/os/GFile.c	2005-05-28 11:04:20.000000000 -0700
@@ -38,7 +38,6 @@
 const INT32 GFMagic = 0x3b7a12f9;
 
 #ifndef __linux__
-extern char *sys_errlist[];
 #endif
 extern int errno;
 
--- tools/include/values.h.orig	1969-12-31 16:00:00.000000000 -0800
+++ tools/include/values.h	2005-05-28 09:44:52.000000000 -0700
@@ -0,0 +1,2 @@
+#include <math.h>
+#include <limits.h>
--- src/data/DataDist.c.org	2009-08-29 14:34:52.000000000 -0400
+++ src/data/DataDist.c	2009-08-29 14:36:50.000000000 -0400
@@ -89,7 +89,7 @@
 {
   TabEntryInter *entryP = p;
 
-  return ((unsigned) entryP->atom1P + (unsigned) entryP->atom2P) % size;
+  return ((unsigned)(uintptr_t) entryP->atom1P + (unsigned)(uintptr_t) entryP->atom2P) % size;
 }
 
 static int