Index: tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz	(revision 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz	(revision 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
@@ -0,0 +1,4 @@
+2
+	Created by molecuilder for --unselect-atoms-inside-sphere test
+H	9.33003	8.57143	9.58
+H	9.33003	11.4286	9.58
Index: tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz
===================================================================
--- tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz	(revision 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz	(revision 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
@@ -0,0 +1,1029 @@
+1027
+	Created by molecuilder on Tue Mar 27 15:00:22 2012, time step 0
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+H	15.0443	17.1429	8.57143
+O	14.2857	17.1429	11.9329
+H	15.0443	17.1429	12.4371
+H	15.0443	17.1429	11.4286
+O	14.2857	17.1429	14.79
+H	15.0443	17.1429	15.2943
+H	15.0443	17.1429	14.2857
+O	14.2857	17.1429	17.6471
+H	15.0443	17.1429	18.1514
+H	15.0443	17.1429	17.1429
+O	17.1429	0	0.504284
+H	17.9015	0	1.00857
+H	17.9015	0	0
+O	17.1429	0	3.36143
+H	17.9015	0	3.86571
+H	17.9015	0	2.85714
+O	17.1429	0	6.21857
+H	17.9015	0	6.72285
+H	17.9015	0	5.71429
+O	17.1429	0	9.07571
+H	17.9015	0	9.58
+H	17.9015	0	8.57143
+O	17.1429	0	11.9329
+H	17.9015	0	12.4371
+H	17.9015	0	11.4286
+O	17.1429	0	14.79
+H	17.9015	0	15.2943
+H	17.9015	0	14.2857
+O	17.1429	0	17.6471
+H	17.9015	0	18.1514
+H	17.9015	0	17.1429
+O	17.1429	2.85714	0.504284
+H	17.9015	2.85714	1.00857
+H	17.9015	2.85714	0
+O	17.1429	2.85714	3.36143
+H	17.9015	2.85714	3.86571
+H	17.9015	2.85714	2.85714
+O	17.1429	2.85714	6.21857
+H	17.9015	2.85714	6.72285
+H	17.9015	2.85714	5.71429
+O	17.1429	2.85714	9.07571
+H	17.9015	2.85714	9.58
+H	17.9015	2.85714	8.57143
+O	17.1429	2.85714	11.9329
+H	17.9015	2.85714	12.4371
+H	17.9015	2.85714	11.4286
+O	17.1429	2.85714	14.79
+H	17.9015	2.85714	15.2943
+H	17.9015	2.85714	14.2857
+O	17.1429	2.85714	17.6471
+H	17.9015	2.85714	18.1514
+H	17.9015	2.85714	17.1429
+O	17.1429	5.71429	0.504284
+H	17.9015	5.71429	1.00857
+H	17.9015	5.71429	0
+O	17.1429	5.71429	3.36143
+H	17.9015	5.71429	3.86571
+H	17.9015	5.71429	2.85714
+O	17.1429	5.71429	6.21857
+H	17.9015	5.71429	6.72285
+H	17.9015	5.71429	5.71429
+O	17.1429	5.71429	9.07571
+H	17.9015	5.71429	9.58
+H	17.9015	5.71429	8.57143
+O	17.1429	5.71429	11.9329
+H	17.9015	5.71429	12.4371
+H	17.9015	5.71429	11.4286
+O	17.1429	5.71429	14.79
+H	17.9015	5.71429	15.2943
+H	17.9015	5.71429	14.2857
+O	17.1429	5.71429	17.6471
+H	17.9015	5.71429	18.1514
+H	17.9015	5.71429	17.1429
+O	17.1429	8.57143	0.504284
+H	17.9015	8.57143	1.00857
+H	17.9015	8.57143	0
+O	17.1429	8.57143	3.36143
+H	17.9015	8.57143	3.86571
+H	17.9015	8.57143	2.85714
+O	17.1429	8.57143	6.21857
+H	17.9015	8.57143	6.72285
+H	17.9015	8.57143	5.71429
+O	17.1429	8.57143	9.07571
+H	17.9015	8.57143	9.58
+H	17.9015	8.57143	8.57143
+O	17.1429	8.57143	11.9329
+H	17.9015	8.57143	12.4371
+H	17.9015	8.57143	11.4286
+O	17.1429	8.57143	14.79
+H	17.9015	8.57143	15.2943
+H	17.9015	8.57143	14.2857
+O	17.1429	8.57143	17.6471
+H	17.9015	8.57143	18.1514
+H	17.9015	8.57143	17.1429
+O	17.1429	11.4286	0.504284
+H	17.9015	11.4286	1.00857
+H	17.9015	11.4286	0
+O	17.1429	11.4286	3.36143
+H	17.9015	11.4286	3.86571
+H	17.9015	11.4286	2.85714
+O	17.1429	11.4286	6.21857
+H	17.9015	11.4286	6.72285
+H	17.9015	11.4286	5.71429
+O	17.1429	11.4286	9.07571
+H	17.9015	11.4286	9.58
+H	17.9015	11.4286	8.57143
+O	17.1429	11.4286	11.9329
+H	17.9015	11.4286	12.4371
+H	17.9015	11.4286	11.4286
+O	17.1429	11.4286	14.79
+H	17.9015	11.4286	15.2943
+H	17.9015	11.4286	14.2857
+O	17.1429	11.4286	17.6471
+H	17.9015	11.4286	18.1514
+H	17.9015	11.4286	17.1429
+O	17.1429	14.2857	0.504284
+H	17.9015	14.2857	1.00857
+H	17.9015	14.2857	0
+O	17.1429	14.2857	3.36143
+H	17.9015	14.2857	3.86571
+H	17.9015	14.2857	2.85714
+O	17.1429	14.2857	6.21857
+H	17.9015	14.2857	6.72285
+H	17.9015	14.2857	5.71429
+O	17.1429	14.2857	9.07571
+H	17.9015	14.2857	9.58
+H	17.9015	14.2857	8.57143
+O	17.1429	14.2857	11.9329
+H	17.9015	14.2857	12.4371
+H	17.9015	14.2857	11.4286
+O	17.1429	14.2857	14.79
+H	17.9015	14.2857	15.2943
+H	17.9015	14.2857	14.2857
+O	17.1429	14.2857	17.6471
+H	17.9015	14.2857	18.1514
+H	17.9015	14.2857	17.1429
+O	17.1429	17.1429	0.504284
+H	17.9015	17.1429	1.00857
+H	17.9015	17.1429	0
+O	17.1429	17.1429	3.36143
+H	17.9015	17.1429	3.86571
+H	17.9015	17.1429	2.85714
+O	17.1429	17.1429	6.21857
+H	17.9015	17.1429	6.72285
+H	17.9015	17.1429	5.71429
+O	17.1429	17.1429	9.07571
+H	17.9015	17.1429	9.58
+H	17.9015	17.1429	8.57143
+O	17.1429	17.1429	11.9329
+H	17.9015	17.1429	12.4371
+H	17.9015	17.1429	11.4286
+O	17.1429	17.1429	14.79
+H	17.9015	17.1429	15.2943
+H	17.9015	17.1429	14.2857
+O	17.1429	17.1429	17.6471
+H	17.9015	17.1429	18.1514
+H	17.9015	17.1429	17.1429
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 93d78e8de4fa69e04316803de231b7406107b2d9)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at	(revision 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
@@ -14,7 +14,7 @@
 AT_SKIP_IF([! cat >/dev/null < /dev/null])  # check whether cat is there
 AT_SKIP_IF([! wc -l /dev/null])  # check whether wc is there
-AT_CHECK([cat < $file | awk -F" " '{ if (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10) > 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
-AT_CHECK([fgrep "507" stdout], 0, [ignore], [ignore])
-AT_CHECK([cat < $file | awk -F" " '{ if (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10) < 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
+AT_CHECK([cat < $file | awk -F" " '{ if ((NF == 4) && (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10)) > 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
+AT_CHECK([fgrep "505" stdout], 0, [ignore], [ignore])
+AT_CHECK([cat < $file | awk -F" " '{ if ((NF == 4) && (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10)) < 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
 AT_CHECK([fgrep "0" stdout], 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 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at	(revision 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
@@ -0,0 +1,45 @@
+### 3. (un)select all atoms inside a tiny sphere
+
+AT_SETUP([Selection - All atoms inside tiny sphere])
+AT_KEYWORDS([selection atom sphere select-atoms-inside-sphere])
+
+file=allatomsoutsidetinysphere.xyz
+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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz], 0, [ignore], [ignore])
+
+# check size of sphere
+AT_SKIP_IF([! awk '' < /dev/null])  # check whether awk is there
+AT_SKIP_IF([! cat >/dev/null < /dev/null])  # check whether cat is there
+AT_SKIP_IF([! wc -l /dev/null])  # check whether wc is there
+AT_CHECK([cat < $file | awk -F" " '{ if ((NF == 4) && (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10)) > 2.7225) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
+AT_CHECK([fgrep "1027" stdout], 0, [ignore], [ignore])
+AT_CHECK([cat < $file | awk -F" " '{ if ((NF == 4) && (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10)) < 2.7225) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
+AT_CHECK([fgrep "0" stdout], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+
+AT_SETUP([Selection - All atoms inside tiny sphere with Undo])
+AT_KEYWORDS([selection atom sphere select-atoms-inside-sphere])
+
+file=allatomsoutsidetinysphere.xyz
+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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/pre/box.xyz], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+
+AT_SETUP([Selection - All atoms inside tiny sphere with Redo])
+AT_KEYWORDS([selection atom sphere select-atoms-inside-sphere])
+
+file=allatomsoutsidetinysphere.xyz
+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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz], 0, [ignore], [ignore])
+
+AT_CLEANUP
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 93d78e8de4fa69e04316803de231b7406107b2d9)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at	(revision 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
@@ -15,7 +15,7 @@
 AT_SKIP_IF([! cat >/dev/null < /dev/null])  # check whether awk is there
 AT_SKIP_IF([! wc -l /dev/null])  # check whether wc is there
-AT_CHECK([cat < $file | awk -F" " '{ if (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10) > 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
-AT_CHECK([fgrep "2" stdout], 0, [ignore], [ignore])
-AT_CHECK([cat < $file | awk -F" " '{ if (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10) < 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
+AT_CHECK([cat < $file | awk -F" " '{ if ((NF == 4) && (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10)) > 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
+AT_CHECK([fgrep "0" stdout], 0, [ignore], [ignore])
+AT_CHECK([cat < $file | awk -F" " '{ if ((NF == 4) && (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10)) < 100) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
 AT_CHECK([fgrep "524" stdout], 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 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
+++ tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at	(revision 3e1b7b6bbc335f8797e72e3edc99ef7639f3b319)
@@ -0,0 +1,45 @@
+### 3. (un)select all atoms inside a tiny sphere
+
+AT_SETUP([Unselection - All atoms inside tiny sphere])
+AT_KEYWORDS([unselection atom sphere unselect-atoms-inside-sphere])
+
+file=allatomsinsidetinysphere.xyz
+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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz], 0, [ignore], [ignore])
+
+# check size of sphere
+AT_SKIP_IF([! awk '' < /dev/null])  # check whether awk is there
+AT_SKIP_IF([! cat >/dev/null < /dev/null])  # check whether cat is there
+AT_SKIP_IF([! wc -l /dev/null])  # check whether wc is there
+AT_CHECK([cat < $file | awk -F" " '{ if ((NF == 4) && (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10) > 2.7225)) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
+AT_CHECK([fgrep "0" stdout], 0, [ignore], [ignore])
+AT_CHECK([cat < $file | awk -F" " '{ if ((NF == 4) && (($2-10)*($2-10)+($3-10)*($3-10)+($4-10)*($4-10) < 2.7225)) print $1,$2,$3,$4;}' | wc -l], 0, [stdout], [ignore])
+AT_CHECK([fgrep "2" stdout], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+
+AT_SETUP([Unselection - All atoms inside tiny sphere with Undo])
+AT_KEYWORDS([unselection atom sphere unselect-atoms-inside-sphere])
+
+file=allatomsinsidetinysphere.xyz
+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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/empty.xyz], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+
+AT_SETUP([Unselection - All atoms inside tiny sphere with Redo])
+AT_KEYWORDS([unselection atom sphere unselect-atoms-inside-sphere])
+
+file=allatomsinsidetinysphere.xyz
+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([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz], 0, [ignore], [ignore])
+
+AT_CLEANUP
