diff --git a/docs/source/index.rst b/docs/source/index.rst
index fc11bdb3678367ec4663391c7b08c47c3ee113b0..90508121b022c4a2094e1354cb1376ed217ddc07 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -165,7 +165,6 @@ Option               Description                                  Values
 output_name          Base name of output files                    **out**, any string
 output               Coordinate output format                     **gro**
 output_xtc           Should a pseudo-CG XTC be created            **False**, True
-map_only             Run in mapping-only mode                     **False**, True
 map_center           Mapping method                               **geom**, mass
 virtual_map_center   Virtual site mapping method                  **geom**, mass
 constr_threshold     Convert stiff bonds to constraints over      **100000**, any number
diff --git a/pycgtool/__main__.py b/pycgtool/__main__.py
index b2b589cd1da379edc251550356e9aede9e69586a..77f770aef424a3606504217f0c12ef7b71252f01 100755
--- a/pycgtool/__main__.py
+++ b/pycgtool/__main__.py
@@ -168,8 +168,6 @@ def parse_arguments(arg_list):
     # Mapping options
     mapping_options = parser.add_argument_group("mapping options")
 
-    mapping_options.add_argument("--map-only", '--no-map-only', default=False, action=BooleanAction,
-                                 help="Run in mapping-only mode?")
     mapping_options.add_argument("--map-center", default="geom",
                                  choices=["geom", "mass", "first"],
                                  help="Mapping method")
@@ -182,7 +180,7 @@ def parse_arguments(arg_list):
     # Bond options
     bond_options = parser.add_argument_group("bond options")
 
-    bond_options.add_argument("--constr_threshold", type=float, default=100000,
+    bond_options.add_argument("--constr-threshold", type=float, default=100000,
                               help="Convert bonds with force constants over [value] to constraints")
     bond_options.add_argument("--temperature", type=float, default=310,
                               help="Temperature of reference simulation")
@@ -227,12 +225,17 @@ def validate_arguments(args):
     """
     if not args.dump_measurements:
         args.dump_measurements = bool(args.bondset) and not bool(args.mapping)
-
-    if not args.map_only:
-        args.map_only = not bool(args.bondset)
+        logger.info(
+            'Argument --dump-measurements has been set because you have provided a bondset but no mapping'
+        )
 
     if not args.mapping and not args.bondset:
-        raise ArgumentValidationError("One or both of -m and -b is required.")
+        raise ArgumentValidationError('One or both of -m and -b is required')
+
+    if args.backmapper_resname:
+        logger.warning(
+            'Backmapping is an experimental feature and has not yet been fully validated'
+        )
 
     return args