Fix: Require chain selection for structure preparation (no default to all chains)

amberprep/js/script.js

@@ -2835,6 +2835,13 @@ echo "Analysis completed! Results saved in analysis/ directory"
             return;
         }
 
+        // Get selected chains first and validate
+        const selectedChains = this.getSelectedChains();
+        if (!selectedChains || selectedChains.length === 0) {
+            alert('Please select at least one chain for structure preparation.');
+            return;
+        }
+
         // Get preparation options
         const options = {
             remove_water: document.getElementById('remove-water').checked,
@@ -2844,7 +2851,7 @@ echo "Analysis completed! Results saved in analysis/ directory"
             add_ace: document.getElementById('add-ace').checked,
             preserve_ligands: document.getElementById('preserve-ligands').checked,
             separate_ligands: document.getElementById('separate-ligands').checked,
-            selected_chains: this.getSelectedChains(),
+            selected_chains: selectedChains,
             selected_ligands: this.getSelectedLigands()
         };
 

amberprep/structure_preparation.py

@@ -735,8 +735,8 @@ def prepare_structure(pdb_content, options, output_dir="output"):
             if not extract_selected_chains(pdb_content, user_chain_file, selected_chains):
                 raise Exception("Failed to extract selected chains")
         else:
-            print("Step 0.5a: No chains selected, using original structure")
-            shutil.copy2(input_file, user_chain_file)
+            # No chains selected - raise an error instead of using all chains
+            raise Exception("No chains selected. Please select at least one chain for structure preparation.")
         
         if selected_ligands:
             ligand_names = []