--- Makefile.am	2008-08-07 04:57:43.000000000 +0200
+++ Makefile.am.new	2009-04-22 13:45:22.000000000 +0200
@@ -104,30 +104,11 @@
 	    mkdir $(CWD)/$$dir/tmp ; \
 	  fi ; \
 	  chmod 777 $(CWD)/$$dir/tmp ; \
-	  echo "Adding server.html" ; \
-	  cp $$c/html/server.html $(CWD)/$$dir/index.html ; \
-	  echo "Adding python files" ; \
-	  cp $$c/*.py* $(CWD)/$$dir/. ; \
+	  cp $$c/main*.py $(CWD)/$$dir/. ; \
 	  echo "Adding __init__.py" ; \
 	  cp $$c/__init__.py $(CWD)/$$dir/__init__.py ; \
 	  echo "Adding pdb2pqr.py" ; \
 	  cp $$c/pdb2pqr.py $(CWD)/$$dir/. ; \
-	  echo "Adding pdb2pqr.cgi" ; \
-	  cp $$c/pdb2pqr.cgi $(CWD)/$$dir/. ; \
-	  echo "Adding pdb2pqr.css" ; \
-	  cp $$c/apbs_cgi.cgi $(CWD)/$$dir/. ; \
-	  echo "Adding apbs_cgi.cgi" ; \
-	  cp $$c/jmol.cgi $(CWD)/$$dir/. ; \
-	  echo "Adding jmol.cgi" ; \
-	  cp $$c/visualize.cgi $(CWD)/$$dir/. ; \
-	  echo "Adding visualize.cgi" ; \
-	  cp $$c/querystatus.cgi $(CWD)/$$dir/. ; \
-	  echo "Adding querystatus.cgi" ; \
-	  cp $$c/Jmol.js $(CWD)/$$dir/. ; \
-	  echo "Adding Jmol.js" ; \
-	  cp $$c/JmolApplet.jar $(CWD)/$$dir/. ; \
-	  echo "Adding JmolApplet.jar" ; \
-	  cp $$c/pdb2pqr.css $(CWD)/$$dir/. ; \
 	  if ! test -d $(CWD)/$$dir/dat  ; then \
 	    mkdir $(CWD)/$$dir/dat ; \
 	  fi ; \
@@ -135,44 +115,11 @@
 	  cp $$c/dat/*.xml $(CWD)/$$dir/dat/. ; \
 	  cp $$c/dat/*.DAT $(CWD)/$$dir/dat/. ; \
 	  cp $$c/dat/*.names $(CWD)/$$dir/dat/. ; \
-	  if ! test -d $(CWD)/$$dir/doc  ; then \
-	    mkdir $(CWD)/$$dir/doc ; \
-	  fi ; \
-	  echo "Adding doc/" ; \
-	  cp $$c/doc/*.html $(CWD)/$$dir/doc/. ; \
-	  cp $$c/doc/*.sh $(CWD)/$$dir/doc/. ; \
-	  if ! test -d $(CWD)/$$dir/doc/images  ; then \
-	    mkdir $(CWD)/$$dir/doc/images ; \
-	  fi ; \
-	  cp $$c/doc/images/*.png $(CWD)/$$dir/doc/images/. ; \
-	  if ! test -d $(CWD)/$$dir/doc/pydoc ; then \
-	    mkdir $(CWD)/$$dir/doc/pydoc ; \
-	  fi ; \
-	  cp $$c/doc/pydoc/*.html $(CWD)/$$dir/doc/pydoc/. ; \
-	  if ! test -d $(CWD)/$$dir/examples ; then \
-	    mkdir $(CWD)/$$dir/examples ; \
-	  fi ; \
-	  echo "Adding examples/" ; \
-	  cp $$c/examples/*.html $(CWD)/$$dir/examples/. ; \
-	  if ! test -d $(CWD)/$$dir/examples/1a1p ; then \
-	    mkdir $(CWD)/$$dir/examples/1a1p ; \
-	  fi ; \
-	  cp $$c/examples/1a1p/*.pdb $(CWD)/$$dir/examples/1a1p/. ; \
-	  cp $$c/examples/1a1p/README $(CWD)/$$dir/examples/1a1p/. ; \
-	  if ! test -d $(CWD)/$$dir/examples/ligands ; then \
-	    mkdir $(CWD)/$$dir/examples/ligands ; \
-	  fi ; \
-	  cp $$c/examples/ligands/*.mol* $(CWD)/$$dir/examples/ligands/. ; \
-	  if ! test -d $(CWD)/$$dir/extensions ; then \
-	    mkdir $(CWD)/$$dir/extensions ; \
-	  fi ; \
 	  echo "Adding extensions" ; \
+	  if ! test -d $(CWD)/$$dir/extensions ; then \
+	    mkdir $(CWD)/$$dir/extensions ; \
+	  fi ; \
 	  cp $$c/extensions/*.py $(CWD)/$$dir/extensions/. ; \
-	  if ! test -d $(CWD)/$$dir/html  ; then \
-	    mkdir $(CWD)/$$dir/html ; \
-	  fi ; \
-	  cp $$c/html/master-index.html $(CWD)/$$dir/html/. ; \
-	  cp $$c/html/server.html $(CWD)/$$dir/html/server.html ; \
 	  if ! test -d $(CWD)/$$dir/src ; then \
 	    mkdir $(CWD)/$$dir/src ; \
 	  fi ; \
--- Makefile.am	2009-04-22 13:48:23.000000000 +0200
+++ Makefile.am.new	2009-04-22 13:49:52.000000000 +0200
@@ -168,49 +168,6 @@
 	  echo PDB2PQR has been installed in $(CWD)/$$dir ; \
 	  echo ; \
 	  cd $(CWD)/$$dir ; \
-	  cd $$c; \
-	  rm lastfieldfile prefixfile dir1file fieldfile ; \
-	  echo $(URL) > url_file ; \
-	  awk -F"/" '{print $$(NF-1)}' url_file > url_file_2 ; \
-	  last_url=`cat url_file_2` ; \
-	  echo $(PREFIX) > p_file ; \
-	  awk -F"/" '{print $$(NF-1)}' p_file > p_file_2 ; \
-	  last_p=`cat p_file_2` ; \
-	  rm -f url_file* p_file* ; \
-	  if test `whoami` = "root" ; then \
-            webviewable="true" ; \
-	    echo ${prefix} > prefix_file_tmp ; \
-            first=`awk -F"/" '{ print $$2 }' prefix_file_tmp` ; \
-	    second=`awk -F"/" '{ print $$3 }' prefix_file_tmp` ; \
-	    third=`awk -F"/" '{ print $$4 }' prefix_file_tmp` ; \
-	    rm -f prefix_file_tmp ; \
-	    if test $$first != var || test $$second != www || test $$third != html ; then  \
-	      webviewable=false ; \
-	    fi ; \
-	    if test "$$last_url" != "$$last_p" || test "$$webviewable" = "false" ; then \
-	      echo Need to make symbolic link between $(PREFIX) and /var/www/html/"$$last_url" ; \
-	      if test -d "/var/www/html/$$last_url" ; then \
-	        echo "***" Warning! Directory /var/www/html/"$$last_url" already exists. ; \
-		echo Do you want to overwrite this? \(Y/N\); \
-		read choice ; \
-	        while (test $$choice != "Y" && test $$choice != "y" && test $$choice != "N" && test $$choice != "n")  \
-	          do  \
-	          echo You have entered $$choice. Please enter Y or N: ; \
-	          read choice ; \
-	        done ; \
-	        if test $$choice = "N" || test $$choice = "n" ; then  \
-	          echo Please run configure again and specify a different --prefix ; \
-	          exit 0 ; \
-	        fi ; \
-	  	rm -rf /var/www/html/"$$last_url" ; \
-	      fi ; \
-	      ln -s $(PREFIX) /var/www/html/"$$last_url" ; \
-	      echo "Symbolic link created." ; \
-	    fi ; \
-	  else  \
-	    echo Ask your system administrator to make a symbolic link in /var/www/html by executing the following command; \
-	    echo ln -s $(PREFIX) /var/www/html/"$$last_url" ; \
-	  fi ; \
 	fi