diff -ur pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu3 pdb-extract-v1.700-prod-src/etc/make.platform.gnu3
--- pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu3	2005-12-19 00:32:21.000000000 -0800
+++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu3	2005-12-19 00:48:25.000000000 -0800
@@ -6,6 +6,8 @@
 ##
 ##########################################################################
 
+LIBDIR= /usr/lib
+
 #-----Lexer and Parser section-------------------------------------------#
 
 # Lexer executable
@@ -89,7 +91,7 @@
 DEFINES=$(GDEFINES) $(LDEFINES)
 
 ## Global include directories
-GINCLUDES= 
+GINCLUDES= -I/usr/include/rcsb
 
 # Collect all include directories from global include directories and
 # include directories specified in module makefile
@@ -107,8 +109,8 @@
 C_WARNINGS=$(WARNINGS)
 
 # C compiler flags
-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
                $(INCLUDES) 
 
 ## C++ compiler
@@ -128,9 +130,9 @@
 EXT=C
 
 # C++ compiler flags
-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
         $(INCLUDES)
-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
                  $(DEFINES) $(INCLUDES)
 # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
 # source code that is not maintained by PDB
@@ -144,7 +146,7 @@
 F77=f77
 
 # Fortran compiler flags
-FFLAGS=-O -u
+FFLAGS=$(F_OPT)
 
 # Additional Fortran libraries
 F77LIBS=
diff -ur pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu4 pdb-extract-v1.700-prod-src/etc/make.platform.gnu4
--- pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu4	2005-12-19 00:32:21.000000000 -0800
+++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu4	2005-12-19 00:48:25.000000000 -0800
@@ -6,6 +6,8 @@
 ##
 ##########################################################################
 
+LIBDIR= /usr/lib
+
 #-----Lexer and Parser section-------------------------------------------#
 
 # Lexer executable
@@ -34,7 +36,7 @@
 
 # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
 # warnings as errors.
-WARNINGS_AS_ERRORS=-Werror
+WARNINGS_AS_ERRORS=
 
 # ALL_WARNINGS defines flags to instruct all compilers to report all
 # warnings.
@@ -90,7 +92,7 @@
 DEFINES=$(GDEFINES) $(LDEFINES)
 
 ## Global include directories
-GINCLUDES= 
+GINCLUDES= -I/usr/include/rcsb
 
 # Collect all include directories from global include directories and
 # include directories specified in module makefile
@@ -108,8 +110,8 @@
 C_WARNINGS=$(WARNINGS)
 
 # C compiler flags
-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
                $(INCLUDES) 
 
 ## C++ compiler
@@ -129,9 +131,9 @@
 EXT=C
 
 # C++ compiler flags
-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
         $(INCLUDES)
-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
                  $(DEFINES) $(INCLUDES)
 # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
 # source code that is not maintained by PDB
@@ -145,7 +147,7 @@
 F77=f77
 
 # Fortran compiler flags
-FFLAGS=-O -u
+FFLAGS=$(F_OPT)
 
 # Additional Fortran libraries
 F77LIBS=
diff -ur pdb-extract-v1.700-prod-src.orig/Makefile pdb-extract-v1.700-prod-src/Makefile
--- pdb-extract-v1.700-prod-src.orig/Makefile	2005-12-19 00:32:21.000000000 -0800
+++ pdb-extract-v1.700-prod-src/Makefile	2005-12-19 00:48:25.000000000 -0800
@@ -22,10 +22,7 @@
 
 DATADIRS = data pdb-extract-data
 
-LIBDIRS =  misclib-v2.1 regex-v2.1 ciflib-common-v3.02 cifobj-common-v4.04 \
-           btree-obj-v3.1 cif-table-obj-v6.1 cifparse-obj-v6.3 \
-           htmllib-v3.1 connect-v2.2 filterlib-v8.2 $(EXTRACT) \
-           validation-v6.2 maxit-v8.2
+LIBDIRS =  maxit-v8.2
 
 all:	compile
 
@@ -60,7 +57,7 @@
 		echo "------------------------------------------------------------"; \
 		echo "**** Making $$libdir ****"; \
 		echo "------------------------------------------------------------"; \
-		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
+		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" install) || exit 1; \
 	done
 
 binary:
diff -ur pdb-extract-v1.700-prod-src.orig/maxit-v8.2/Makefile pdb-extract-v1.700-prod-src/maxit-v8.2/Makefile
--- pdb-extract-v1.700-prod-src.orig/maxit-v8.2/Makefile	2005-12-19 00:32:21.000000000 -0800
+++ pdb-extract-v1.700-prod-src/maxit-v8.2/Makefile	2005-12-19 00:51:46.000000000 -0800
@@ -33,35 +33,35 @@
 #----------------------------------------------------------------------------
 include ../etc/Makefile.platform
 
-LIBS    = $(LIBINSTDIR)/libvalidation.a \
-          $(LIBINSTDIR)/libndbfilter.a \
-          $(LIBINSTDIR)/libconnect.a \
-          $(LIBINSTDIR)/libciffileobj.a \
-          $(LIBINSTDIR)/libcifobj.a \
-          $(LIBINSTDIR)/libistable.a \
-          $(LIBINSTDIR)/libregex.a \
-          $(LIBINSTDIR)/libtblindex.a \
-          $(LIBINSTDIR)/libcifstr.a \
-          $(LIBINSTDIR)/libndbmisc.a
-
-LIBS1   = $(LIBINSTDIR)/liberfiolib.a \
-          $(LIBINSTDIR)/liberfutil.a \
-          $(LIBINSTDIR)/libciffileobj.a \
-          $(LIBINSTDIR)/libcifobj.a \
-          $(LIBINSTDIR)/libistable.a \
-          $(LIBINSTDIR)/libtblindex.a \
-          $(LIBINSTDIR)/libcifstr.a \
-          $(LIBINSTDIR)/libndbmisc.a
-
-LIBS2   = $(LIBINSTDIR)/liberfiolib.a \
-          $(LIBINSTDIR)/libconnect.a \
-          $(LIBINSTDIR)/libciffileobj.a \
-          $(LIBINSTDIR)/libcifobj.a \
-          $(LIBINSTDIR)/libistable.a \
-          $(LIBINSTDIR)/libregex.a \
-          $(LIBINSTDIR)/libtblindex.a \
-          $(LIBINSTDIR)/libcifstr.a \
-          $(LIBINSTDIR)/libndbmisc.a
+LIBS    = $(LIBDIR)/libvalidation.a \
+          $(LIBDIR)/libndbfilter.a \
+          $(LIBDIR)/libconnect.a \
+          $(LIBDIR)/libciffileobj.a \
+          $(LIBDIR)/libcifobj.a \
+          $(LIBDIR)/libistable.a \
+          $(LIBDIR)/libregex.a \
+          $(LIBDIR)/libtblindex.a \
+          $(LIBDIR)/libcifstr.a \
+          $(LIBDIR)/libndbmisc.a
+
+LIBS1   = $(LIBDIR)/liberfiolib.a \
+          $(LIBDIR)/liberfutil.a \
+          $(LIBDIR)/libciffileobj.a \
+          $(LIBDIR)/libcifobj.a \
+          $(LIBDIR)/libistable.a \
+          $(LIBDIR)/libtblindex.a \
+          $(LIBDIR)/libcifstr.a \
+          $(LIBDIR)/libndbmisc.a
+
+LIBS2   = $(LIBDIR)/liberfiolib.a \
+          $(LIBDIR)/libconnect.a \
+          $(LIBDIR)/libciffileobj.a \
+          $(LIBDIR)/libcifobj.a \
+          $(LIBDIR)/libistable.a \
+          $(LIBDIR)/libregex.a \
+          $(LIBDIR)/libtblindex.a \
+          $(LIBDIR)/libcifstr.a \
+          $(LIBDIR)/libndbmisc.a
 #
 NDBLIB     = $(LIB)/libmaxit.a
 #