diff --git a/src/petab_gui/controllers/mother_controller.py b/src/petab_gui/controllers/mother_controller.py
index b9ec028..a1003ee 100644
--- a/src/petab_gui/controllers/mother_controller.py
+++ b/src/petab_gui/controllers/mother_controller.py
@@ -822,6 +822,7 @@ def new_file(self):
                 controller.clear_model()
                 continue
             controller.clear_table()
+        self.view.plot_dock.plot_it()
 
     def check_model(self):
         """Check the consistency of the model. And log the results."""
diff --git a/src/petab_gui/models/pandas_table_model.py b/src/petab_gui/models/pandas_table_model.py
index 93400b8..32124c2 100644
--- a/src/petab_gui/models/pandas_table_model.py
+++ b/src/petab_gui/models/pandas_table_model.py
@@ -728,6 +728,13 @@ def clear_table(self):
         """Clear all data from the table."""
         self.beginResetModel()
         self._data_frame.drop(self._data_frame.index, inplace=True)
+        self._data_frame.drop(
+            self._data_frame.columns.difference(
+                COLUMNS[self.table_type].keys()
+            ),
+            axis=1,
+            inplace=True,
+        )
         self.endResetModel()
 
     def check_selection(self):