diff -ur -x make-sparky sparky.orig/bin/sparky sparky/bin/sparky
--- sparky.orig/bin/sparky	2004-03-05 11:32:10.000000000 -0800
+++ sparky/bin/sparky	2005-12-17 17:36:51.000000000 -0800
@@ -4,22 +4,10 @@
 #
 
 # -----------------------------------------------------------------------------
-# Figure out Sparky installation directory from $0.
-#
-set sparky_exe = $0
-while (-l $sparky_exe)
-  set ls_sparky_exe = `ls -l "$sparky_exe"`
-  set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'`
-end
-set sparky_bin = `dirname "$sparky_exe"`
-set sparky_bin = `cd "$sparky_bin"; pwd`
-set sparky_inst = `dirname "$sparky_bin"`
-
-# -----------------------------------------------------------------------------
 # Sparky uses the SPARKY_INSTALL environment variable to find its
 # application resource file and print prolog file.
 #
-setenv SPARKY_INSTALL		$sparky_inst
+setenv SPARKY_INSTALL		@GENTOO_PORTAGE_EPREFIX@/usr/lib/sparky
 
 # -----------------------------------------------------------------------------
 # If Python is available start Sparky as a Python extension.
diff -ur -x make-sparky sparky.orig/c++/Makefile sparky/c++/Makefile
--- sparky.orig/c++/Makefile	2004-02-03 15:56:24.000000000 -0800
+++ sparky/c++/Makefile	2005-12-18 10:49:08.000000000 -0800
@@ -22,6 +22,7 @@
 PYTHON_PREFIX	= /usr/local
 PYTHON_LIB	= $(PYTHON_PREFIX)/lib/python$(PYTHON_VERSION)
 PYTHON_INC	= $(PYTHON_PREFIX)/include/python$(PYTHON_VERSION)
+PYDIR		= $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
 TCLTK_VERSION	= 8.4
 TCLTK_VER_WIN32	= 84
 TK_PREFIX	= /usr/local
@@ -113,21 +114,20 @@
 
 nopython: $(EXECUTABLES)
 
-install-python: $(SPY_PYMOD) $(TKINTER_PYMOD) $(SPARKY_INSTALL)/python \
-  $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk
-	$(INSTALL) $(SPY_PYMOD) $(SPARKY_INSTALL)/python/sparky
-	chmod 755 $(SPARKY_INSTALL)/python/sparky/$(SPY_PYMOD)
-	$(INSTALL) $(TKINTER_PYMOD) $(SPARKY_INSTALL)/python/lib-tk
-	chmod 755 $(SPARKY_INSTALL)/python/lib-tk/$(TKINTER_PYMOD)
+install-python: $(SPY_PYMOD) $(TKINTER_PYMOD) $(PYDIR) \
+	$(PYDIR)/sparky $(PYDIR)/lib-tk
+	$(INSTALL) $(SPY_PYMOD) $(PYDIR)/sparky
+	chmod 755 $(PYDIR)/sparky/$(SPY_PYMOD)
+	$(INSTALL) $(TKINTER_PYMOD) $(PYDIR)/lib-tk
+	chmod 755 $(PYDIR)/lib-tk/$(TKINTER_PYMOD)
 
 install-nopython: $(EXECUTABLES) $(SPARKY_INSTALL)/bin
 	$(INSTALL) $(EXECUTABLES) $(SPARKY_INSTALL)/bin
 	cd $(SPARKY_INSTALL)/bin ; \
 	chmod 755 $(EXECUTABLES)
 
-$(SPARKY_INSTALL)/bin $(SPARKY_INSTALL)/python \
-$(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk:
-	mkdir $@
+$(SPARKY_INSTALL)/bin $(PYDIR) $(PYDIR)/sparky $(PYDIR)/lib-tk:
+	mkdir -p $@
 	chmod 755 $@
 
 sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS)
diff -ur -x make-sparky sparky.orig/c++/paths.h sparky/c++/paths.h
--- sparky.orig/c++/paths.h	2002-01-17 19:15:06.000000000 -0800
+++ sparky/c++/paths.h	2005-12-17 20:57:15.000000000 -0800
@@ -19,7 +19,7 @@
 // Installation subdirectories and files
 //
 #define SPARKY_MANUAL		"manual"
-#define SPARKY_LIB		"lib"
+#define SPARKY_LIB		""
 #define SPARKY_PRINT		"print-prolog.ps"	// under lib directory
 #define SPARKY_RESOURCE		"Sparky"		// under lib directory
 #define SPARKY_SAMPLE_DATA	"example"
diff -ur -x make-sparky sparky.orig/c++/system-unix.cc sparky/c++/system-unix.cc
--- sparky.orig/c++/system-unix.cc	2004-02-26 10:57:54.000000000 -0800
+++ sparky/c++/system-unix.cc	2005-12-17 20:56:58.000000000 -0800
@@ -95,7 +95,7 @@
 //
 Stringy default_sparky_install_path()
 {
-  return file_path(file_path(file_path("", "usr"), "local"), "sparky");
+  return file_path(file_path(file_path("", "usr"), "lib"), "sparky");
 }
 
 // ----------------------------------------------------------------------------
diff -ur -x make-sparky sparky.orig/lib/Makefile sparky/lib/Makefile
--- sparky.orig/lib/Makefile	2004-02-18 10:53:29.000000000 -0800
+++ sparky/lib/Makefile	2005-12-17 16:03:21.000000000 -0800
@@ -18,9 +18,9 @@
 TCL_SHLIB	= lib$(TCL_VERSION)$(TCLTK_SHLIB_SUFFIX)
 TK_SHLIB	= lib$(TK_VERSION)$(TCLTK_SHLIB_SUFFIX)
 
-install: $(SPARKY_INSTALL)/lib install-tcl-tk
-	$(INSTALL) Sparky print-prolog.ps $(SPARKY_INSTALL)/lib
-	cd $(SPARKY_INSTALL)/lib ; \
+install: $(SPARKY_INSTALL)/lib
+	$(INSTALL) Sparky print-prolog.ps $(SPARKY_INSTALL)/lib/sparky
+	cd $(SPARKY_INSTALL)/lib/sparky ; \
 	chmod 644 Sparky print-prolog.ps
 
 install-tcl-tk: $(SPARKY_INSTALL)/lib
diff -ur -x make-sparky sparky.orig/Makefile sparky/Makefile
--- sparky.orig/Makefile	2004-02-18 10:40:04.000000000 -0800
+++ sparky/Makefile	2005-12-17 19:40:48.000000000 -0800
@@ -40,18 +40,22 @@
 
 PYTHON_VERSION	= 2.3
 PYTHON_DIR	= 
+PYDIR		= $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
 
 PYMOD_SUFFIX	= .so
 SPY_PYMOD	= spy$(PYMOD_SUFFIX)
 TKINTER_PYMOD	= _tkinter$(PYMOD_SUFFIX)
 
+PYDIR       = $(SPARKY_INSTALL)/lib/sparky/python
+DOCDIR		= $(SPARKY_INSTALL)/share/doc/sparky
+
 all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force
 	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@
 
 Makefile.dep TAGS: force
 	cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@
 
-install: install-nopython $(SPARKY_INSTALL) install-python
+install: install-nopython $(SPARKY_INSTALL)
 	cd $(SPARKY_OBJ) && \
 	$(MAKE) -f $(SPARKY_SRC)/Makefile -e install-python
 	cd $(SPARKY)/python && $(MAKE) -f Makefile -e install
@@ -67,7 +71,8 @@
 	chmod 755 sparky$(SCRIPT_SUFFIX)
 
 install-example: $(SPARKY_INSTALL)
-	cd $(SPARKY) ; $(INSTALLDIR) example $(SPARKY_INSTALL)
+	mkdir -p $(DOCDIR)/example
+	cd $(SPARKY) ; $(INSTALLDIR) example $(DOCDIR)
 
 install-lib: $(SPARKY_INSTALL)
 	cd $(SPARKY)/lib && $(MAKE) -f Makefile -e install
@@ -76,21 +81,14 @@
 	cd $(SPARKY)/manual && $(MAKE) -f Makefile -e install
 
 install-misc: $(SPARKY_INSTALL)
-	cd $(SPARKY) ; $(INSTALL) LICENSE README $(SPARKY_INSTALL)
-	cd $(SPARKY_INSTALL) ; chmod 644 LICENSE README
-
-install-python: $(SPARKY_INSTALL) $(SPARKY_INSTALL)/python$(PYTHON_VERSION)
-ifdef PYTHON_DIR
-	$(INSTALLDIR) $(PYTHON_DIR)/* $(SPARKY_INSTALL)/python$(PYTHON_VERSION)
-else
-	echo "Not packaging Python with Sparky."
-endif
+	cd $(SPARKY) ; $(INSTALL) LICENSE README $(DOCDIR)
+	cd $(DOCDIR) ; chmod 644 LICENSE README
 
 install-mac:
 	cd $(SPARKY)/mac && $(MAKE) -f Makefile -e install
 
-$(SPARKY_INSTALL) $(SPARKY_INSTALL)/bin $(SPARKY_INSTALL)/python$(PYTHON_VERSION):
-	mkdir $@
+$(SPARKY_INSTALL) $(SPARKY_INSTALL)/bin $(PYDIR):
+	mkdir -p $@
 	chmod 755 $@
 
 force:
diff -ur -x make-sparky sparky.orig/manual/Makefile sparky/manual/Makefile
--- sparky.orig/manual/Makefile	2004-03-08 15:40:06.000000000 -0800
+++ sparky/manual/Makefile	2005-12-17 19:37:45.000000000 -0800
@@ -13,6 +13,8 @@
 
 SPARKY_INSTALL	= /usr/local/sparky
 MANUAL_WWW	= /usr/local/html/cgl/sparky/manual
+DOCDIR		= $(SPARKY_INSTALL)/share/doc/sparky
+MANUAL_LOC = $(DOCDIR)/manual
 
 MANUAL_SECTIONS = overview.html intro.html views.html peaks.html \
 		  extensions.html autoassign.html misc.html \
@@ -45,17 +47,17 @@
 
 all: $(MANUAL_FILES)
 
-install: $(MANUAL_FILES) $(SPARKY_INSTALL)/manual \
-		$(SPARKY_INSTALL)/manual/images
-	$(INSTALL) $(MANUAL_FILES) $(SPARKY_INSTALL)/manual
-	cd $(SPARKY_INSTALL)/manual ; \
+install: $(MANUAL_FILES) $(MANUAL_LOC) \
+		$(MANUAL_LOC)/images
+	$(INSTALL) $(MANUAL_FILES) $(MANUAL_LOC)
+	cd $(MANUAL_LOC) ; \
 	chmod 644 $(MANUAL_FILES)
 	cd images ; \
-	$(INSTALL) $(IMAGE_FILES) $(SPARKY_INSTALL)/manual/images
-	cd $(SPARKY_INSTALL)/manual/images ; \
+	$(INSTALL) $(IMAGE_FILES) $(MANUAL_LOC)/images
+	cd $(MANUAL_LOC)/images ; \
 	chmod 644 $(IMAGE_FILES)
 
-$(SPARKY_INSTALL)/manual $(SPARKY_INSTALL)/manual/images:
+$(MANUAL_LOC) $(MANUAL_LOC)/images:
 	mkdir $@
 	chmod 755 $@
 
Only in sparky/manual: manual-postscript.gz
diff -ur -x make-sparky sparky.orig/python/Makefile sparky/python/Makefile
--- sparky.orig/python/Makefile	2004-02-18 10:51:06.000000000 -0800
+++ sparky/python/Makefile	2005-12-17 19:43:06.000000000 -0800
@@ -9,6 +9,8 @@
 PYTHON_VERSION	= 2.3
 PYTHON		= $(PYTHON_PREFIX)/bin/python$(PYTHON_VERSION)
 PYTHON_LIB	= $(PYTHON_PREFIX)/lib/python$(PYTHON_VERSION)
+PYDIR		= $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
+DOCDIR		= $(SPARKY_INSTALL)/share/doc/sparky
 
 PYTHON_CODE	= __init__.py align.py assigngraph.py atomnames.py \
 		  atoms.py autoassign.py axes.py \
@@ -27,18 +29,13 @@
 		  sputil.py start_in_chimera.py strips.py subprocess.py \
 		  tkutil.py volumeerror.py xeasy.py xplor.py
 
-install: $(SPARKY_INSTALL)/python $(SPARKY_INSTALL)/python/sparky \
-		$(SPARKY_INSTALL)/python/lib-tk
-	$(INSTALL) README $(SPARKY_INSTALL)/python
-	$(INSTALL) $(PYTHON_CODE) $(SPARKY_INSTALL)/python/sparky
-	$(INSTALL) lib-tk/*.py $(SPARKY_INSTALL)/python/lib-tk
-	chmod 644 $(SPARKY_INSTALL)/python/README
-	cd $(SPARKY_INSTALL)/python/sparky ; chmod 644 $(PYTHON_CODE)
-	chmod 644 $(SPARKY_INSTALL)/python/lib-tk/*.py
-	$(PYTHON) $(PYTHON_LIB)/compileall.py $(SPARKY_INSTALL)/python/sparky
-	$(PYTHON) $(PYTHON_LIB)/compileall.py $(SPARKY_INSTALL)/python/lib-tk
+install: $(PYDIR) $(PYDIR)/sparky $(DOCDIR)/python
+	$(INSTALL) README $(DOCDIR)/python
+	$(INSTALL) $(PYTHON_CODE) $(PYDIR)/sparky
+	chmod 644 $(DOCDIR)/python/README
+	cd $(PYDIR)/sparky ; chmod 644 $(PYTHON_CODE)
 
-$(SPARKY_INSTALL)/python $(SPARKY_INSTALL)/python/sparky \
-  $(SPARKY_INSTALL)/python/lib-tk:
+$(PYDIR) $(PYDIR)/sparky \
+  $(PYDIR)/lib-tk $(DOCDIR)/python:
 	mkdir $@
 	chmod 755 $@
diff -ur -x make-sparky sparky.orig/python/spingraph.py sparky/python/spingraph.py
--- sparky.orig/python/spingraph.py	2001-12-17 10:51:10.000000000 -0800
+++ sparky/python/spingraph.py	2005-12-17 22:09:17.000000000 -0800
@@ -831,7 +831,7 @@
                'by creating a file specifying atom positions, colors,\n' +
                'sizes, and text label positions.  Sparky provides a\n' +
                'default layout file\n' +
-               '\n\t/usr/local/sparky/python/spinlayout.py\n\n' +
+               '\n\t/usr/lib/python*/site-packages/sparky/python/spinlayout.py\n\n' +
                'You override this file by making your own copy\n' +
                '\n\t~/Sparky/Python/spinlayout.py\n\n' +
                'You can create the desired template on the screen\n'