Index: tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at	(revision ff9e5aa00cb3a198f58315ad4dda3952ed5b34eb)
+++ tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at	(revision 842aac61c6439ac82216b2a76ac58cea36787afe)
@@ -42,5 +42,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
 
@@ -63,5 +63,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-shape-by-name "cube1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz], 0, [ignore], [ignore])
 
@@ -75,5 +75,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --select-shape-by-name "cube1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
 
Index: tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at	(revision ff9e5aa00cb3a198f58315ad4dda3952ed5b34eb)
+++ tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at	(revision 842aac61c6439ac82216b2a76ac58cea36787afe)
@@ -41,5 +41,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
 
@@ -62,5 +62,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz], 0, [ignore], [ignore])
 
@@ -74,5 +74,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --select-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --select-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsoutsidecuboid.xyz], 0, [ignore], [ignore])
 
Index: tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at	(revision ff9e5aa00cb3a198f58315ad4dda3952ed5b34eb)
+++ tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at	(revision 842aac61c6439ac82216b2a76ac58cea36787afe)
@@ -42,5 +42,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume 0 -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume 0 -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsinsidecuboid.xyz], 0, [ignore], [ignore])
 
@@ -63,5 +63,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume  --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/empty.xyz], 0, [ignore], [ignore])
 
@@ -75,5 +75,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "cube1" --select-shape-by-name "cube1" --unselect-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "cube1" --shape-type "cube" --translation "0,0,0" --stretch "10, 10, 10" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "cube1" --unselect-atoms-inside-volume  --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideCuboid/post/allatomsinsidecuboid.xyz], 0, [ignore], [ignore])
 
Index: tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at	(revision ff9e5aa00cb3a198f58315ad4dda3952ed5b34eb)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at	(revision 842aac61c6439ac82216b2a76ac58cea36787afe)
@@ -41,5 +41,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidesphere.xyz], 0, [ignore], [ignore])
 
@@ -62,5 +62,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz], 0, [ignore], [ignore])
 
@@ -74,5 +74,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10., 10., 10." --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidesphere.xyz], 0, [ignore], [ignore])
 
Index: tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at	(revision ff9e5aa00cb3a198f58315ad4dda3952ed5b34eb)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at	(revision 842aac61c6439ac82216b2a76ac58cea36787afe)
@@ -41,5 +41,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz], 0, [ignore], [ignore])
 
@@ -62,5 +62,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz], 0, [ignore], [ignore])
 
@@ -74,5 +74,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --select-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz], 0, [ignore], [ignore])
 
Index: tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at	(revision ff9e5aa00cb3a198f58315ad4dda3952ed5b34eb)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at	(revision 842aac61c6439ac82216b2a76ac58cea36787afe)
@@ -42,5 +42,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume  -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume  -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidesphere.xyz], 0, [ignore], [ignore])
 
@@ -63,5 +63,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/empty.xyz], 0, [ignore], [ignore])
 
@@ -75,5 +75,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "10,10,10"  --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidesphere.xyz], 0, [ignore], [ignore])
 
Index: tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at	(revision ff9e5aa00cb3a198f58315ad4dda3952ed5b34eb)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at	(revision 842aac61c6439ac82216b2a76ac58cea36787afe)
@@ -41,5 +41,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz], 0, [ignore], [ignore])
 
@@ -62,5 +62,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/empty.xyz], 0, [ignore], [ignore])
 
@@ -74,5 +74,5 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz $file], 0)
 AT_CHECK([chmod u+w $file], 0)
-AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --set-shape --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --create-shape --shape-name "sphere1" --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -v 5 --select-all-atoms --create-shape --shape-name "sphere1" --shape-type "sphere" --translation "10,10,10" --stretch "1.65, 1.65, 1.65" --angle-x 0. --angle-y 0. --angle-z 0. --select-shape-by-name "sphere1" --unselect-atoms-inside-volume --undo --redo -r], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz], 0, [ignore], [ignore])
 
