diff --git a/CodonSubst.R b/CodonSubst.R
index cc98697..158d973 100644
--- a/CodonSubst.R
+++ b/CodonSubst.R
@@ -37,8 +37,6 @@
 #	p<-CodonSubst()
 #	# build rate matrix from paml file
 #	# buildFromPAML(p,"path_to_paml_file")	# do not run this
-#	# set a rate
-#	setRate(p,"A->D",2)
 #	# get object summary	
 #	summary(p)
 # }
diff --git a/pkg/man/CodonSubst.Rd b/pkg/man/CodonSubst.Rd
index 604b4e3..bd43aa1 100644
--- a/pkg/man/CodonSubst.Rd
+++ b/pkg/man/CodonSubst.Rd
@@ -85,8 +85,6 @@ $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCa
 	p<-CodonSubst()
 	# build rate matrix from paml file
 	# buildFromPAML(p,"path_to_paml_file")	# do not run this
-	# set a rate
-	setRate(p,"A->D",2)
 	# get object summary
 	summary(p)
  }