--- configure.in_orig	2010-01-27 16:15:51.387782244 -0800
+++ configure.in	2010-01-27 16:44:53.586783325 -0800
@@ -132,13 +132,26 @@
 AM_PATH_GLUT(, [echo You need the GLUT utility library; exit 1], AC_MSG_ERROR([Cannot find proper GLUT version]))
 
 dnl Check for MMDB.
-AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
+# AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
 
-AM_WITH_MMDBSSM
+# AM_WITH_MMDBSSM
+PKG_CHECK_MODULES(MMDB, mmdb >= 1.12)
+MMDB_CXXFLAGS="-DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP $MMDB_CFLAGS"
+AC_SUBST(MMDB_CXXFLAGS)
+AC_SUBST(MMDB_LIBS)
+
+PKG_CHECK_MODULES(MMDBSSM, ssm >= 0.1)
+MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB $MMDBSSM_CFLAGS"
+AC_SUBST(MMDBSSM_CXXFLAGS)
+AC_SUBST(MMDBSSM_LIBS)
 
 dnl Check for Clipper.  we exit if clipper is not found.
 #
-AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
+# AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
+PKG_CHECK_MODULES(CLIPPER, clipper >= 2.0)
+CLIPPER_CXXFLAGS=$CLIPPER_CFLAGS
+AC_SUBST(CLIPPER_CXXFLAGS)
+AC_SUBST(CLIPPER_LIBS)
 
 # we set default coot_guile to true
 coot_guile=true
@@ -146,7 +159,7 @@
 if test x$coot_guile = xtrue ; then
    GUILE_FLAGS
    AM_GUILE_LIB
-   AM_GUILE_GUI
+#   AM_GUILE_GUI
    GUILE_VERSION=$($ac_cv_path_GUILE_CONFIG --version  2>&1 | awk '{split($NF, arr, "[[.]]");  print arr[[1]] "." arr[[2]]}')
    echo checking GUILE_VERSION: $GUILE_VERSION
    AC_SUBST(GUILE_VERSION)