diff --git a/src/protein_shapes/prot_domain_classifier/prot_domain_classifier.py b/src/protein_shapes/prot_domain_classifier/prot_domain_classifier.py
index c3a22cd..6a6bde7 100755
--- a/src/protein_shapes/prot_domain_classifier/prot_domain_classifier.py
+++ b/src/protein_shapes/prot_domain_classifier/prot_domain_classifier.py
@@ -43,14 +43,14 @@
 else:
     ref_embed_dir = output_dir / f"embeddings_{ref_suffix}"
     subprocess.run(
-        ["python", cur_dir / "embed.py", reference_structures, ref_embed_dir]
+        [sys.executable, cur_dir / "embed.py", reference_structures, ref_embed_dir]
     )
     _, ref_embeds = load_embeddings(ref_embed_dir)
 
 samp_embed_dir = output_dir / f"embeddings_{samp_suffix}"
 
 if embed_samples != "precomputed":
-    subprocess.run(["python", cur_dir / "embed.py", sampled_structures, samp_embed_dir])
+    subprocess.run([sys.executable, cur_dir / "embed.py", sampled_structures, samp_embed_dir])
 else:
     samp_embed_dir = sampled_structures
 
diff --git a/src/protein_shapes/proteinmpnn/embed.py b/src/protein_shapes/proteinmpnn/embed.py
index e7a88e0..3b73c2f 100755
--- a/src/protein_shapes/proteinmpnn/embed.py
+++ b/src/protein_shapes/proteinmpnn/embed.py
@@ -2,7 +2,7 @@
 from pathlib import Path
 import os
 import subprocess
-
+import sys
 
 def main():
     parser = argparse.ArgumentParser(
@@ -20,7 +20,7 @@ def main():
     run_script = cur_dir / "run.py"
 
     clean_command = [str(clean_script), args.directory]
-    generate_json_command = ["python", str(generate_json_script), args.directory]
+    generate_json_command = [sys.executable, str(generate_json_script), args.directory]
     # print(f"gen command: {generate_json_command}")
 
     # subprocess.run(clean_command, check=True)
diff --git a/src/protein_shapes/proteinmpnn/proteinmpnn.py b/src/protein_shapes/proteinmpnn/proteinmpnn.py
index 715ec48..e6ad20a 100755
--- a/src/protein_shapes/proteinmpnn/proteinmpnn.py
+++ b/src/protein_shapes/proteinmpnn/proteinmpnn.py
@@ -49,7 +49,7 @@
 else:
     ref_embed_dir = output_dir / f"embeddings_{ref_suffix}"
     subprocess.run(
-        ["python", cur_dir / "embed.py", reference_structures, ref_embed_dir]
+        [sys.executable, cur_dir / "embed.py", reference_structures, ref_embed_dir]
     )
     _, ref_embeds = load_embeddings(ref_embed_dir)
     ref_embeds = np.transpose(ref_embeds, (1, 0, 2))
@@ -57,7 +57,7 @@
 samp_embed_dir = output_dir / f"embeddings_{samp_suffix}"
 
 if embed_samples != "precomputed":
-    subprocess.run(["python", cur_dir / "embed.py", sampled_structures, samp_embed_dir])
+    subprocess.run([sys.executable, cur_dir / "embed.py", sampled_structures, samp_embed_dir])
 else:
     samp_embed_dir = sampled_structures