diff --git a/docs/prediction.md b/docs/prediction.md
index b33d2d0e2..997f5cc3d 100644
--- a/docs/prediction.md
+++ b/docs/prediction.md
@@ -168,8 +168,8 @@ Examples of common options include:
 | `--msa_server_url`       | str             | `https://api.colabfold.com` | MSA server url. Used only if --use_msa_server is set.                                                                                                                               |
 | `--msa_pairing_strategy` | str             | `greedy`                    | Pairing strategy to use. Used only if --use_msa_server is set. Options are 'greedy' and 'complete'                                                                                  |
 | `--use_potentials`        | `FLAG`          | `False`                     | Whether to run the original Boltz-2 model using inference time potentials.                                                                                                        |
-| `--write_full_pae`       | `FLAG`          | `False`                     | Whether to save the full PAE matrix as a file.                                                                                                                                      |
-| `--write_full_pde`       | `FLAG`          | `False`                     | Whether to save the full PDE matrix as a file.                                                                                                                                      |
+| `--write_full_pae` <br> `--no_write_full_pae`       | `FLAG`          | `True`                     | Whether to save the full PAE matrix as a file.                                                                                                                                      |
+| `--write_full_pde` <br> `--no_write_full_pde`       | `FLAG`          | `True`                     | Whether to save the full PDE matrix as a file.                                                                                                                                      |
 
 ## Output
 
diff --git a/src/boltz/main.py b/src/boltz/main.py
index 4a3750fec..648bb7ecc 100644
--- a/src/boltz/main.py
+++ b/src/boltz/main.py
@@ -887,15 +887,17 @@ def cli() -> None:
     default=None,
 )
 @click.option(
-    "--write_full_pae",
+    "--write_full_pae/--no_write_full_pae",
     type=bool,
     is_flag=True,
+    default=True,
     help="Whether to dump the pae into a npz file. Default is True.",
 )
 @click.option(
-    "--write_full_pde",
+    "--write_full_pde/--no_write_full_pde",
     type=bool,
     is_flag=True,
+    default=True,
     help="Whether to dump the pde into a npz file. Default is False.",
 )
 @click.option(
@@ -1054,8 +1056,8 @@ def predict(  # noqa: C901, PLR0915, PLR0912
     diffusion_samples_affinity: int = 3,
     max_parallel_samples: Optional[int] = None,
     step_scale: Optional[float] = None,
-    write_full_pae: bool = False,
-    write_full_pde: bool = False,
+    write_full_pae: bool = True,
+    write_full_pde: bool = True,
     output_format: Literal["pdb", "mmcif"] = "mmcif",
     num_workers: int = 2,
     override: bool = False,
diff --git a/src/boltz/model/models/boltz2.py b/src/boltz/model/models/boltz2.py
index d42f3400c..33bc3e71f 100644
--- a/src/boltz/model/models/boltz2.py
+++ b/src/boltz/model/models/boltz2.py
@@ -1080,7 +1080,8 @@ def predict_step(self, batch: Any, batch_idx: int, dataloader_idx: int = 0) -> d
             pred_dict["coords"] = out["sample_atom_coords"]
             if self.confidence_prediction:
                 # pred_dict["confidence"] = out.get("ablation_confidence", None)
-                pred_dict["pde"] = out["pde"]
+                if self.predict_args.get("write_full_pde", True):
+                    pred_dict["pde"] = out["pde"]
                 pred_dict["plddt"] = out["plddt"]
                 pred_dict["confidence_score"] = (
                     4 * out["complex_plddt"]
@@ -1098,7 +1099,8 @@ def predict_step(self, batch: Any, batch_idx: int, dataloader_idx: int = 0) -> d
                 pred_dict["complex_pde"] = out["complex_pde"]
                 pred_dict["complex_ipde"] = out["complex_ipde"]
                 if self.alpha_pae > 0:
-                    pred_dict["pae"] = out["pae"]
+                    if self.predict_args.get("write_full_pae", True):
+                        pred_dict["pae"] = out["pae"]
                     pred_dict["ptm"] = out["ptm"]
                     pred_dict["iptm"] = out["iptm"]
                     pred_dict["ligand_iptm"] = out["ligand_iptm"]