diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index 32333d1601245e3c17bec85923cd043c05e5f621..bea0f2d4778a98e34d8da8a9b93dcef1f15fb67a 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -2,6 +2,8 @@ import typer
 import sys
 import re
 import shutil
+import csv
+import yaml
 from typing_extensions import Annotated
 from typing import Optional, List
 from pathlib import Path
@@ -78,13 +80,35 @@ def lint(
 
 @app.command()
 def structure(
+    stat: Annotated[
+        Path,
+        typer.Option(
+            exists=True,
+            file_okay=True,
+            dir_okay=True,
+            writable=False,
+            readable=True,
+            resolve_path=True,
+        ),
+    ],
+    map: Annotated[
+        Path,
+        typer.Option(
+            exists=True,
+            file_okay=True,
+            dir_okay=True,
+            writable=False,
+            readable=True,
+            resolve_path=True,
+        ),
+    ],
     dir: Annotated[
         Path,
         typer.Option(
             exists=True,
             file_okay=False,
             dir_okay=True,
-            writable=False,
+            writable=True,
             readable=True,
             resolve_path=True,
         ),
@@ -101,13 +125,30 @@ def structure(
         ),
     ],
 ):
-    console.rule(f"[bold blue]{dir.name}", style="blue")
-    for f in dir.iterdir():
-        console.print(f"[green] {f.name}")
-        # get the system name
-        system = re.split("_|\.|-0", f.name)[0].lower()
-
-        console.print(system)
-        systemDir = output / system
-        systemDir.mkdir(parents=True, exist_ok=True)
-        shutil.copy2(f, systemDir)
+    with open(map, "r") as map_f:
+        system_to_dir = yaml.safe_load(map_f)
+
+    with open(stat, "r") as stat_f:
+        reader = csv.DictReader(stat_f)
+
+        for row in reader:
+            dir_name = system_to_dir[row["system"]]
+            # console.rule(f"[bold blue]{dir_name}", style="blue")
+            files = [
+                {"f": Path(row["pdb"]), "d": "PDB"},
+                {"f": Path(row["pae_table"]), "d": "PAE"},
+                {"f": Path(row["fasta_file"]), "d": "Fastas"},
+                {"f": Path(row["Foldseek_name"]), "d": "foldseek_monomers_html"},
+            ]
+            target_dir = output / dir_name
+            target_dir.mkdir(parents=True, exist_ok=True)
+            for f in files:
+                str_f = str(f["f"])
+                if str_f and str_f != "." and str_f != "" and str_f != "na":
+                    # console.print("--" + str(f["f"]) + "--")
+                    # console.print(f"[green] copy {f['f'].name} to {target_dir}")
+                    file_to_copy = dir / f["d"] / f["f"]
+                    if file_to_copy.exists():
+                        shutil.copy2(file_to_copy, target_dir)
+                    else:
+                        console.print(f"[red] file {str(file_to_copy.name)} does not exist")
diff --git a/packages/df-wiki-cli/pyproject.toml b/packages/df-wiki-cli/pyproject.toml
index 320115fc3a887382a669362e1118c0a5c2e4f373..236029026cd480779937ff757858d6cf7c8ad037 100644
--- a/packages/df-wiki-cli/pyproject.toml
+++ b/packages/df-wiki-cli/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "df-wiki-cli"
-version = "0.1.2"
+version = "0.1.3"
 description = ""
 authors = ["Remi  PLANEL <rplanel@pasteur.fr>"]
 readme = "README.md"