diff --git a/barnaba/functions.py b/barnaba/functions.py
index d228077..47ef4c5 100644
--- a/barnaba/functions.py
+++ b/barnaba/functions.py
@@ -1236,57 +1236,36 @@ def parse_dotbracket(threshold, file, weights):
           #      mult_chain = True
         if not line.startswith("#"):
             l = line.split()
-            if "pdb" in l[0].lower():
-                dotbr = l[1]
-                if len(dotbr) != len(sequence):
-                    print(mult_chain)
-                    if not mult_chain:
-                        sys.exit("Dot-bracket length does not match sequence length")
-                    else:
-                        dotbr = dotbr[:len(sequence)]
-                base_pairs = parse_dotbr(dotbr)
-                for bp in base_pairs:
-                    ann_list[bp[0], bp[1], "WCc"] = 1.
-                list_base_pairs = base_pairs    
-                ann_lists.append(dict(ann_list))
-                ann_list = {}
-            else:
-                try: int(l[0])
-                except ValueError:
-                    continue
+            dotbr = l[1]
+            if len(dotbr) != len(sequence):
+                if not mult_chain:
+                    sys.exit("Dot-bracket length does not match sequence length")    
                 else:
-                    traj = True
-                    dotbr = l[1]
-                    if len(dotbr) != len(sequence):
-                        if not mult_chain:
-                            sys.exit("Dot-bracket length does not match sequence length")    
-                        else:
-                            dotbr = dotbr[:len(sequence)]
-                    n_frames += 1
-                    base_pairs = parse_dotbr(dotbr)
-                    for bp in base_pairs:
-                        if bp not in list_base_pairs:
-                            list_base_pairs.append(bp)
-                        try:
-                            ann_list[bp[0], bp[1], "WCc"]
-                        except:
-                            if len(weights) == 0:
-                                ann_list[bp[0], bp[1], "WCc"] = 1.
-                            else:
-                                ann_list[bp[0], bp[1], "WCc"] = weights[n_frames-1]
-                        else: 
-                            if len(weights) == 0:
-                                ann_list[bp[0], bp[1], "WCc"] += 1.
-                            else:    
+                    dotbr = dotbr[:len(sequence)]
+            n_frames += 1
+            base_pairs = parse_dotbr(dotbr)
+            for bp in base_pairs:
+                if bp not in list_base_pairs:
+                    list_base_pairs.append(bp)
+                try:
+                    ann_list[bp[0], bp[1], "WCc"]
+                except:
+                    if len(weights) == 0:
+                        ann_list[bp[0], bp[1], "WCc"] = 1.
+                    else:
+                        ann_list[bp[0], bp[1], "WCc"] = weights[n_frames-1]
+                else: 
+                    if len(weights) == 0:
+                        ann_list[bp[0], bp[1], "WCc"] += 1.
+                    else:    
                                 ann_list[bp[0], bp[1], "WCc"] += weights[n_frames-1]
     if len(list_base_pairs) == 0:
         sys.exit("No basepairs found.")
-    if traj:
-        for ann, value in ann_list.items():
-            if len(weights) == 0:
-                ann_list[ann] /= n_frames
-            else:
-                ann_list[ann] /= sum(weights)
+    for ann, value in ann_list.items():
+        if len(weights) == 0:
+            ann_list[ann] /= n_frames
+        else:
+            ann_list[ann] /= sum(weights)
     chains = [0]
     return sequence, ann_list, list_base_pairs, n_frames    
 
diff --git a/bin/barnaba b/bin/barnaba
index 066d37d..1c5de0f 100755
--- a/bin/barnaba
+++ b/bin/barnaba
@@ -316,15 +316,18 @@ def annotate(args):
         for i in range(len(args.pdbs)):
             st, pair, res = bb.annotate(args.pdbs[i])
             stri_p += "# SEQ " + (" ".join([f for f in res]) + "\n")
+            stri_p += "# sequence %s\n" % "-".join(res)
             stri_p += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
             stri_p += "".join([ "%-10s %-10s %4s \n" % (res[pair[0][0][e][0]],res[pair[0][0][e][1]],pair[0][1][e]) for e in range(len(pair[0][0]))])
             
+            stri_s += "# sequence %s\n" % "-".join(res)
             stri_s += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
             stri_s += "".join([ "%-10s %-10s %4s \n" % (res[st[0][0][e][0]],res[st[0][0][e][1]],st[0][1][e]) for e in range(len(st[0][0]))])
 
             if(args.dotbr):
                 dotbr,ss = bb.dot_bracket(pair,res)
                 stri_dot += "# SEQ %s" % ss
+                stri_dot += "# sequence %s\n" % "-".join(res)
                 stri_dot += "%-20s %s\n" %(args.pdbs[i].split("/")[-1],dotbr[0])
 
             
@@ -724,13 +727,13 @@ def sec_structure(args):
     output += "%8d%10.2e%10.2e%10.2e%10d\n" % (i, E, max_F, h, r_i) 
     print( i, " steps of minmization")    
     output += "%d steps of minmization\n" % (i)
-    from scipy.linalg import expm3, norm
+    from scipy.linalg import expm, norm
 
     av_stem_vector = np.mean([pos[int(param_stem[0][1])], pos[int(param_stem[0][2])]], axis=0) - np.mean([pos[int(param_stem[len(param_stem)-1][1])], pos[int(param_stem[len(param_stem)-1][2])]], axis=0)
     theta = np.arctan2(-av_stem_vector[0], -av_stem_vector[1])
 
     def M(axis, theta):
-        return expm3(np.cross(np.eye(3), axis/norm(axis)*theta))
+        return expm(np.cross(np.eye(3), axis/norm(axis)*theta))
     axis = [0,0,1]
     m0 = M(axis, theta)
     trans_pos = np.full((len(pos),3), [dimensions*.5, dimensions*.5, 0])