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 6253ed4bcfa0dd23c33719d286276be9760ec373)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at	(revision 14549870ead800ed0ce73e795e339010dca476a7)
@@ -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-atoms-inside-sphere 10 --position "10,10,10" -r], 0, [stdout], [stderr])
+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. --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 --select-atoms-inside-sphere 10 --position "10,10,10" --undo -r], 0, [stdout], [stderr])
+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. --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 --select-atoms-inside-sphere 10 --position "10,10,10" --undo --redo -r], 0, [stdout], [stderr])
+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. --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 6253ed4bcfa0dd23c33719d286276be9760ec373)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at	(revision 14549870ead800ed0ce73e795e339010dca476a7)
@@ -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-atoms-inside-sphere 1.65 --position "10,10,10" -r], 0, [stdout], [stderr])
+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. --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 --select-atoms-inside-sphere 1.65 --position "10,10,10" --undo -r], 0, [stdout], [stderr])
+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. --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 --select-atoms-inside-sphere 1.65 --position "10,10,10" --undo --redo -r], 0, [stdout], [stderr])
+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. --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 6253ed4bcfa0dd23c33719d286276be9760ec373)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at	(revision 14549870ead800ed0ce73e795e339010dca476a7)
@@ -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 --unselect-atoms-inside-sphere 10 --position "10,10,10" -r], 0, [stdout], [stderr])
+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. --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 --unselect-atoms-inside-sphere 10 --position "10,10,10" --undo -r], 0, [stdout], [stderr])
+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. --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 --unselect-atoms-inside-sphere 10 --position "10,10,10" --undo --redo -r], 0, [stdout], [stderr])
+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. --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 6253ed4bcfa0dd23c33719d286276be9760ec373)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at	(revision 14549870ead800ed0ce73e795e339010dca476a7)
@@ -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 --unselect-atoms-inside-sphere 1.65 --position "10,10,10" -r], 0, [stdout], [stderr])
+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. --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 --unselect-atoms-inside-sphere 1.65 --position "10,10,10" --undo -r], 0, [stdout], [stderr])
+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. --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 --unselect-atoms-inside-sphere 1.65 --position "10,10,10" --undo --redo -r], 0, [stdout], [stderr])
+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. --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])
 
