diff --git a/Makefile b/Makefile
index b84853f..275c227 100644
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,9 @@
 all: closure-compiler/build/compiler.jar js/fornac.js
 
-js/fornac.js:
+js/fornac.js: src/*.js
 	java -jar closure-compiler/build/compiler.jar --compilation_level=SIMPLE_OPTIMIZATIONS --js_output_file=js/fornac.js src/*.js
 
-closure-compiler/build/compiler.jar:
+closure-compiler/build/compiler.jar: closure-compiler/*
 	git submodule init closure-compiler
 	git submodule update closure-compiler
 	cd closure-compiler; ant jar
diff --git a/css/fornac.css b/css/fornac.css
index 670ef25..633f329 100644
--- a/css/fornac.css
+++ b/css/fornac.css
@@ -24,7 +24,7 @@ circle.outline_node {
 }
 
 circle.protein {
-    fill: blue;
+    fill: gray;
     fill-opacity: 0.5;
     stroke-width: 4;
 }
diff --git a/src/fornaf.js b/src/fornaf.js
index 5d41426..5d827b5 100644
--- a/src/fornaf.js
+++ b/src/fornaf.js
@@ -1116,17 +1116,25 @@ function FornaContainer(element, passedOptions) {
         link_lines.append("svg:title")
         .text(link_key);
 
-        link_lines.attr("class", "link")
+        link_lines
+        .classed("link", true)
         .attr("x1", function(d) { return d.source.x; })
         .attr("y1", function(d) { return d.source.y; })
         .attr("x2", function(d) { return d.target.x; })
         .attr("y2", function(d) { return d.target.y; })
         .attr("link_type", function(d) { return d.link_type; } )
+        .attr("class", function(d) { return d3.select(this).attr('class') + " " + d.link_type; })
         .attr('pointer-events', function(d) { if (d.link_type == 'fake') return 'none'; else return 'all';});
 
+        all_links.attr('class', '')
+        .classed('link', true)
+        .attr("link_type", function(d) { return d.link_type; } )
+        .attr("class", function(d) { return d3.select(this).attr('class') + " " + d.link_type; })
+
             all_links.exit().remove();
 
             /* We don't need to update the positions of the stabilizing links */
+            /*
             basepair_links = vis_links.selectAll("[link_type=basepair]");
             basepair_links.classed("basepair", true);
             
@@ -1138,7 +1146,7 @@ function FornaContainer(element, passedOptions) {
 
             plink = vis_links.selectAll("[link_type=protein_chain],[link_type=chain_chain]");
             plink.classed("chain_chain", true);
-
+            */
 
             if (self.displayFakeLinks)
                 xlink = all_links;
@@ -1188,7 +1196,6 @@ function FornaContainer(element, passedOptions) {
                 return node_tooltips[d.node_type];
             };
 
-
             xlink.on('click', link_click);
 
             var circle_update = gnodes.select('circle');
diff --git a/src/simplernaplot.js b/src/simplernaplot.js
index 208ffc2..2f88d2e 100644
--- a/src/simplernaplot.js
+++ b/src/simplernaplot.js
@@ -78,6 +78,7 @@ simple_xy_coordinates = function(pair_table)
           loop(k, l, pair_table);
       }
   }
+
   polygon = Math.PI*(count-2)/count; /* bending angle in loop polygon */
   remember[++r] = j;
   begin = i_old < 0 ? 0 : i_old;
@@ -110,6 +111,5 @@ simple_xy_coordinates = function(pair_table)
       alpha += Math.PI-angle[i+1];
   }
 
-
   return poss;
 }