diff --git a/src/boltz/data/feature/featurizerv2.py b/src/boltz/data/feature/featurizerv2.py
index 2fcb30713..454b28daf 100644
--- a/src/boltz/data/feature/featurizerv2.py
+++ b/src/boltz/data/feature/featurizerv2.py
@@ -1800,6 +1800,7 @@ def process_template_features(
 
         for template in templates:
             offset = template.template_st - template.query_st
+            query_templated_segments = set(range(template.query_st, template.query_en))
 
             # Get query and template tokens to map residues
             query_tokens = data.tokens
@@ -1810,7 +1811,7 @@ def process_template_features(
             # Get the template tokens at the query residues
             chain_id = tmpl_chain_name_to_asym_id[template.template_chain]
             toks = template_tokens[template_tokens["asym_id"] == chain_id]
-            toks = [t for t in toks if t["res_idx"] - offset in q_indices]
+            toks = [t for t in toks if t["res_idx"] - offset in query_templated_segments]
             for t in toks:
                 q_idx = q_indices[t["res_idx"] - offset]
                 row_tokens.append(
diff --git a/src/boltz/data/parse/schema.py b/src/boltz/data/parse/schema.py
index ecff892c3..cd39f534a 100644
--- a/src/boltz/data/parse/schema.py
+++ b/src/boltz/data/parse/schema.py
@@ -523,17 +523,25 @@ def get_local_alignments(query: str, template: str) -> list[Alignment]:
     """
     aligner = Align.PairwiseAligner(scoring="blastp")
     aligner.mode = "local"
-    aligner.open_gap_score = -1000
-    aligner.extend_gap_score = -1000
+    # Biopython blastp default gap score
+    aligner.open_gap_score = -12.0
+    aligner.extend_gap_score = -1.0
 
     alignments = []
-    for result in aligner.align(query, template):
-        coordinates = result.coordinates
+    # Take first alignment as the "best" alignment
+    result = aligner.align(query, template)[0]
+    coordinates = result.coordinates
+    for ipos in range(0, coordinates.shape[1] - 1):
+        query_st, query_en = coordinates[0, ipos:ipos+2]
+        template_st, template_en = coordinates[1, ipos:ipos+2]
+        if query_st == query_en or template_st == template_en:
+            # insertion or deltion, skip the chunk
+            continue
         alignment = Alignment(
-            query_st=int(coordinates[0][0]),
-            query_en=int(coordinates[0][1]),
-            template_st=int(coordinates[1][0]),
-            template_en=int(coordinates[1][1]),
+            query_st=int(query_st),
+            query_en=int(query_en),
+            template_st=int(template_st),
+            template_en=int(template_en)
         )
         alignments.append(alignment)