diff --git a/ipsae.py b/ipsae.py
index 45f64de..b32f3c4 100644
--- a/ipsae.py
+++ b/ipsae.py
@@ -694,7 +694,7 @@ def classify_chains(chains, residue_types):
         ptm_matrix_d0chn=ptm_func_vec(pae_matrix,d0chn[chain1][chain2])
 
         valid_pairs_iptm = (chains == chain2)
-        valid_pairs_matrix = (chains == chain2) & (pae_matrix < pae_cutoff)
+        valid_pairs_matrix = np.outer(chains == chain1, chains == chain2) & (pae_matrix < pae_cutoff)
 
         for i in range(numres):
 
@@ -740,7 +740,7 @@ def classify_chains(chains, residue_types):
         ptm_matrix_d0dom = np.zeros((numres,numres))
         ptm_matrix_d0dom = ptm_func_vec(pae_matrix,d0dom[chain1][chain2])
 
-        valid_pairs_matrix = (chains == chain2) & (pae_matrix < pae_cutoff)
+        valid_pairs_matrix = np.outer(chains == chain1, chains == chain2) & (pae_matrix < pae_cutoff)
 
         # Assuming valid_pairs_matrix is already defined
         n0res_byres_all = np.sum(valid_pairs_matrix, axis=1)