diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
index eb3ba4064d9c95eb47fbe472cfad6a19c948dd64..3ec7908b328c66a044f13366c8074173c55fae59 100644
--- a/modules/mol/alg/doc/molck.rst
+++ b/modules/mol/alg/doc/molck.rst
@@ -107,7 +107,7 @@ It can also be split into subsequent commands for greater controll:
 API
 ###
 
-.. class:: MolckSettings(rm_unk_atoms=False, rm_non_std=False, \
+.. class:: MolckSettings(rm_unk_atoms=True, rm_non_std=False, \
                          rm_hyd_atoms=True, rm_oxt_atoms=False, \
                          rm_zero_occ_atoms=False, colored=False, \
                          map_nonstd_res=True, assign_elem=True)
diff --git a/modules/mol/alg/pymod/export_molck.cc b/modules/mol/alg/pymod/export_molck.cc
index aa50a674f6775536e05ce38796f4a0458c1826a5..039d97e07053ccb7b283b0ab351bd2b718035bf3 100644
--- a/modules/mol/alg/pymod/export_molck.cc
+++ b/modules/mol/alg/pymod/export_molck.cc
@@ -33,7 +33,7 @@ object MolckSettingsInitWrapper(tuple args, dict kwargs){
   object self = args[0];
   args = tuple(args.slice(1,_));
 
-  bool rm_unk_atoms = false;
+  bool rm_unk_atoms = true;
   if(kwargs.contains("rm_unk_atoms")){
     rm_unk_atoms = extract<bool>(kwargs["rm_unk_atoms"]);
     kwargs["rm_unk_atoms"].del();
diff --git a/modules/mol/alg/src/molck.hh b/modules/mol/alg/src/molck.hh
index 145171b8e88b5c35111a47366c0f0d3a996cfcbe..69dc0d5a824a423b0a60cfd16b9f5f8dd5f1abcd 100644
--- a/modules/mol/alg/src/molck.hh
+++ b/modules/mol/alg/src/molck.hh
@@ -45,7 +45,7 @@ struct MolckSettings{
   bool map_nonstd_res;
   bool assign_elem;
 
-  MolckSettings(bool init_rm_unk_atoms=false,
+  MolckSettings(bool init_rm_unk_atoms=true,
                 bool init_rm_non_std=false,
                 bool init_rm_hyd_atoms=true,
                 bool init_rm_oxt_atoms=false,