diff --git a/src/dlstbx/services/trigger.py b/src/dlstbx/services/trigger.py
index bfe986ea4..8c6f31c60 100644
--- a/src/dlstbx/services/trigger.py
+++ b/src/dlstbx/services/trigger.py
@@ -250,6 +250,7 @@ class MultiplexReprocessingParameters(pydantic.BaseModel):
     dcid: int = pydantic.Field(gt=0)
     wavelength: Optional[float] = pydantic.Field(default=None, gt=0)
     spacegroup: Optional[str] = None
+    small_molecule: Optional[bool] = None
     automatic: Optional[bool] = False
     comment: Optional[str] = None
     wavelength_tolerance: float = pydantic.Field(default=1e-4, ge=0)
@@ -2311,6 +2312,7 @@ def trigger_multiplex_reprocessing(
         - dcid: the dataCollectionId for the given data collection
         - wavelength: wavelength of data collection
         - spacegroup: space group for processing
+        - small_molecule: whether or not the data should be processed using small molecule space groups / shelx output files
         - wavelength_tolerance: tolerance for selecting datasets with same wavelength
         - comment: a comment to be stored in the ProcessingJob.comment field
         - automatic: boolean value passed to ProcessingJob.automatic field
@@ -2388,6 +2390,7 @@ def trigger_multiplex_reprocessing(
             "cchalf_filtering_method",
             "image_group_size",
             "sd_cutoff",
+            "small_molecule",
         )
 
         for param_name, param_value in parameters:
diff --git a/src/dlstbx/wrapper/xia2_multiplex.py b/src/dlstbx/wrapper/xia2_multiplex.py
index ba084e463..7bdd973d0 100644
--- a/src/dlstbx/wrapper/xia2_multiplex.py
+++ b/src/dlstbx/wrapper/xia2_multiplex.py
@@ -295,9 +295,15 @@ def is_final_result(final_file: pathlib.Path) -> bool:
             ".sca": None,
             ".bib": "log",
             ".phil": "log",
+            ".hkl": None,
+            ".ins": None,
+            ".cif": None,
         }
         keep = {
             "scaled.mtz": "result",
+            "scaled.ins": "result",
+            "scaled.hkl": "result",
+            "scaled.cif": "result",
             "scaled_unmerged.mtz": "result",
             "scaled.expt": "result",
             "scaled.refl": "result",
@@ -484,6 +490,9 @@ def is_final_result(final_file: pathlib.Path) -> bool:
                                     "scaled.mtz",
                                     "xia2.multiplex.html",
                                     "xia2.multiplex.log",
+                                    "scaled.hkl",
+                                    "scaled.ins",
+                                    "scaled.cif",
                                 )
                             )
                             else 2
diff --git a/src/dlstbx/wrapper/xia2_multiplex_filtering.py b/src/dlstbx/wrapper/xia2_multiplex_filtering.py
index 83baff961..12855f5a3 100644
--- a/src/dlstbx/wrapper/xia2_multiplex_filtering.py
+++ b/src/dlstbx/wrapper/xia2_multiplex_filtering.py
@@ -141,6 +141,7 @@ def construct_commandline(self, params, multiplex_directory):
                 "spacegroup",
                 "anomalous",
                 "absorption_level",
+                "small_molecule",  # This will be taken from the parent phil
             }
             translation = {
                 "d_min": "resolution.d_min",
@@ -256,9 +257,15 @@ def is_final_result(final_file: pathlib.Path) -> bool:
             ".mtz": None,
             ".html": "log",
             ".sca": None,
+            ".ins": None,
+            ".hkl": None,
+            ".cif": None,
         }
         keep = {
             "filtered.mtz": "result",
+            "filtered.ins": "result",
+            "filtered.hkl": "result",
+            "filtered.cif": "result",
             "filtered_unmerged.mtz": "result",
             "filtered.expt": "result",
             "filtered.refl": "result",
@@ -392,6 +399,9 @@ def is_final_result(final_file: pathlib.Path) -> bool:
                                         "filtered.mtz",
                                         "xia2.multiplex_filtering.html",
                                         "xia2.multiplex_filtering.log",
+                                        "filtered.ins",
+                                        "filtered.hkl",
+                                        "filtered.cif",
                                     )
                                 )
                                 else 2