diff --git a/diffpy/srreal01/applications/colorFromOverlap.py b/diffpy/srreal01/applications/colorFromOverlap.py
index 9f929d9a..8bc9288c 100755
--- a/diffpy/srreal01/applications/colorFromOverlap.py
+++ b/diffpy/srreal01/applications/colorFromOverlap.py
@@ -13,6 +13,8 @@
                             not specified, use composition from structfile1.
   -l, --latpar=a,b,c,A,B,G  override lattice parameters in structfiles.
   -o, --outstru=FILE        Filename for saving the best fitting structure.
+                            Write to the standard output when "-" and suppress
+                            any other output.
       --outfmt=FORMAT       Output format for outstru, by default "discus"
                             Can be any format supported by diffpy.Structure.
   -r, --radia=A1:r1,...     Redefine element radia.  By default use covalent
@@ -30,6 +32,7 @@
 __id__ = "$Id$"
 
 import sys
+import logging
 
 # global variables
 gl_doc = __doc__
@@ -48,6 +51,15 @@
         "V",    "version",
 ]
 
+# output logger
+outlog = logging.getLogger("colorFromOverlap")
+outlog.setLevel(logging.INFO)
+ch = logging.StreamHandler(sys.stdout)
+ch.setFormatter(logging.Formatter("%(message)s"))
+outlog.addHandler(ch)
+del ch
+
+
 class ColorFromOverlap(object):
     """Class for running overlap optimization script.
     """
@@ -104,11 +116,11 @@ def run(self):
             optcost, optstru = self.optimizeColoring(stru)
             self.optimized_costs.append(optcost)
             self.optimized_structures.append(optstru)
-            print f, optcost, getcoloring(optstru)
+            outlog.info("%s %g %r", f, optcost, getcoloring(optstru))
         cbest, fbest, strubest = min(zip(
             self.optimized_costs, self.structfiles, self.optimized_structures))
-        print "# BEST " + (78 - 7) * '-'
-        print fbest, cbest, getcoloring(strubest)
+        outlog.info("# BEST " + (78 - 7) * '-')
+        outlog.info("%s %g %r", fbest, cbest, getcoloring(strubest))
         self.saveOutstru()
         return
 
@@ -214,7 +226,7 @@ def optimizeColoring(self, stru):
         # use initialAtomConflicts to setup proper atom radii
         ac = self.initialAtomConflicts(stru)
         # undo site shuffling
-        ac.setStructure(stru)
+        ac.setSiteColoring(self.expanded_formula)
         coststru = [(self.cost(ac), ac.getStructure())]
         for i in range(self.repeats):
             ac0 = self.initialAtomConflicts(stru)
@@ -256,7 +268,11 @@ def saveOutstru(self):
         from numpy import argmin
         idx = argmin(self.optimized_costs)
         stru = self.optimized_structures[idx]
-        stru.write(self.outstru, format=self.outfmt)
+        if self.outstru == '-':
+            s = stru.writeStr(format=self.outfmt)
+            sys.stdout.write(s)
+        else:
+            stru.write(self.outstru, format=self.outfmt)
         return
 
 
@@ -379,6 +395,8 @@ def _parseOption_latpar(self, a):
 
     def _parseOption_outstru(self, a):
         self.outstru = a
+        if self.outstru == "-":
+            outlog.setLevel(logging.WARNING)
         return
 
     def _parseOption_outfmt(self, a):
@@ -459,6 +477,10 @@ def main():
             raise
         print >> sys.stderr, err
         sys.exit(2)
+    return
+
 
 if __name__ == "__main__":
     main()
+
+# End of file