diff --git a/chai_lab/data/dataset/msas/load.py b/chai_lab/data/dataset/msas/load.py
index 5e177ed..7b29045 100644
--- a/chai_lab/data/dataset/msas/load.py
+++ b/chai_lab/data/dataset/msas/load.py
@@ -20,6 +20,7 @@
     parse_aligned_pqt_to_msa_context,
 )
 from chai_lab.data.parsing.msas.data_source import MSADataSource
+from chai_lab.data.parsing.structure.entity_type import EntityType
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -43,14 +44,14 @@ def get_msa_contexts(
 
     # MSAs are constructed based on sequence, so use the unique sequences present
     # in input chains to determine the MSAs that need to be loaded
-
-    def get_msa_contexts_for_seq(seq) -> MSAContext:
+    def get_msa_contexts_for_seq(seq: str, etype: EntityType) -> MSAContext:
         path = msa_directory / expected_basename(seq)
-        if not path.is_file():
-            if seq != "X":
-                # Don't warn for the special "X" sequence
+        # If the MSA is missing, or the query is not a protein, return an empty MSA
+        if not path.is_file() or etype != EntityType.PROTEIN:
+            if etype == EntityType.PROTEIN:
+                # Warn for proteins that have missing MSAs
                 logger.warning(f"No MSA found for sequence: {seq}")
-            [tokenized_seq] = tokenize_sequences_to_arrays([seq])[0]
+            [tokenized_seq], _ = tokenize_sequences_to_arrays([seq])
             return MSAContext.create_single_seq(
                 MSADataSource.QUERY, tokens=torch.from_numpy(tokenized_seq)
             )
@@ -61,9 +62,9 @@ def get_msa_contexts_for_seq(seq) -> MSAContext:
     # For each chain, either fetch the corresponding MSA or create an empty MSA if it is missing
     # + reindex to handle residues that are tokenized per-atom (this also crops if necessary)
     msa_contexts = [
-        get_msa_contexts_for_seq(chain.entity_data.sequence)[
-            :, chain.structure_context.token_residue_index
-        ]
+        get_msa_contexts_for_seq(
+            seq=chain.entity_data.sequence, etype=chain.entity_data.entity_type
+        )[:, chain.structure_context.token_residue_index]
         for chain in chains
     ]
 
diff --git a/chai_lab/main.py b/chai_lab/main.py
index 124a94d..8132d65 100644
--- a/chai_lab/main.py
+++ b/chai_lab/main.py
@@ -10,6 +10,8 @@
 
 from chai_lab.chai1 import run_inference
 
+logging.basicConfig(level=logging.INFO)
+
 CITATION = """
 @article{Chai-1-Technical-Report,
 	title        = {Chai-1: Decoding the molecular interactions of life},
@@ -38,5 +40,4 @@ def cli():
 
 
 if __name__ == "__main__":
-    logging.basicConfig(level=logging.INFO)
     cli()