diff --git a/Biobase/FR3D.hs b/Biobase/FR3D.hs
--- a/Biobase/FR3D.hs
+++ b/Biobase/FR3D.hs
@@ -14,6 +14,7 @@
 import Data.ByteString.Char8 as BS
 import Data.List as L
 
+import Biobase.Primary
 import Biobase.Secondary
 
 
@@ -47,7 +48,7 @@
 data LinFR3D = LinFR3D
   { pdbID :: ByteString
   , sequence :: ByteString
-  , pairs :: [ExtPairIdx] -- [(Int,Int,String)] -- TODO String -> CWW ?!
+  , pairs :: [(ExtPairIdx,ExtPair)] -- we keep the ExtPair information as provided by the non-linearized FR3D data
   } deriving (Show)
 
 -- | The default format is a bit unwieldy; Linearization assumes that all
@@ -62,10 +63,13 @@
   } where
       trans = snd $ L.mapAccumL ( \acc (x,y) -> (acc + 1 + BS.length y, (x,acc))
                                 ) 0 chains
-      f Basepair{..} =  ( ( maybe (-1) (\v -> v+seqpos1) $ L.lookup chain1 trans
-                          , maybe (-1) (\v -> v+seqpos2) $ L.lookup chain2 trans )
-                        , interaction
-                        )
+      f Basepair{..} =  (pi,p) where
+        pi = ( ( maybe (-1) (\v -> v+seqpos1) $ L.lookup chain1 trans
+               , maybe (-1) (\v -> v+seqpos2) $ L.lookup chain2 trans
+               )
+             , interaction
+             )
+        p = ( (mkNuc nucleotide1, mkNuc nucleotide2), interaction )
 
 class RemoveDuplicatePairs a where
   removeDuplicatePairs :: a -> a
@@ -75,5 +79,44 @@
     f Basepair{..} = (chain1,seqpos1) < (chain2,seqpos2)
 
 instance RemoveDuplicatePairs LinFR3D where
-  removeDuplicatePairs x@LinFR3D{..} = x{pairs = L.filter f pairs} where
+  removeDuplicatePairs x@LinFR3D{..} = x{pairs = L.filter (f.fst) pairs} where
     f ((x,y),_) = x<y
+
+
+
+-- ** Checking data structures
+
+-- | Checks an FR3D file for correctness. Returns either a Left on errors or
+-- Right FR3D if correct.
+--
+-- TODO chain existence check
+
+checkFR3D fr3d@FR3D{..}
+  | L.null xs = Right fr3d
+  | otherwise = Left (fr3d,xs)
+  where
+    xs = [ x
+         | x <- basepairs
+         , let Just c1 = lookup (chain1 x) chains
+         , let Just c2 = lookup (chain2 x) chains
+         ,  seqpos1 x < 0
+         || seqpos2 x < 0
+         || seqpos1 x >= BS.length c1
+         || seqpos2 x >= BS.length c2
+         || nucleotide1 x /= c1 `BS.index` seqpos1 x
+         || nucleotide2 x /= c2 `BS.index` seqpos2 x
+         ]
+
+checkLinFR3D linfr3d@LinFR3D{..}
+  | L.null xs = Right linfr3d
+  | otherwise = Left (linfr3d,xs)
+  where
+    xs = [ x
+         | x@(pi,p) <- pairs
+         ,  baseL pi < 0
+         || baseR pi < 0
+         || baseL pi >= BS.length sequence
+         || baseR pi >= BS.length sequence
+         || mkNuc (sequence `BS.index` baseL pi) /= baseL p
+         || mkNuc (sequence `BS.index` baseR pi) /= baseR p
+         ]
diff --git a/Biobase/FR3D/Import.hs b/Biobase/FR3D/Import.hs
--- a/Biobase/FR3D/Import.hs
+++ b/Biobase/FR3D/Import.hs
@@ -1,3 +1,4 @@
+{-# LANGUAGE RecordWildCards #-}
 {-# LANGUAGE OverloadedStrings #-}
 
 -- | Importing of FR3D data. Both "basepairs" and "near interactions" are
@@ -14,6 +15,7 @@
 import Data.Iteratee.ListLike as I
 import Data.List as L
 import Data.Maybe
+import qualified Data.Map as M
 import System.FilePath.Find as F
 
 import Biobase.Secondary
@@ -30,15 +32,26 @@
   f = do
     I.head -- fr3d header
     I.head -- sequence header
-    cs <- I.break ((/="#") . BS.take 1)
+    cs' <- I.break ((/="#") . BS.take 1)
     I.head -- basepairs header
     xs <- stream2list -- and all basepairs
+    let cs = L.map (second (BS.drop 1) . BS.span isAlphaNum . BS.drop 2) $ cs'
     return FR3D
       { pdbid = maybe "" (BS.take 4) $ listToMaybe xs
-      , chains = L.map (second (BS.drop 1) . BS.span isAlphaNum . BS.drop 2) cs
-      , basepairs = L.map bs2basepair $ xs
+      , chains = cs
+      , basepairs = {- L.map (fixSeqpos cs) . -} L.map bs2basepair $ xs
       }
 
+{-
+ - This would be for fixing sequence position information, but it seems that
+ - FR3D does not store this info consistently...
+ -
+fixSeqpos :: [(ByteString,ByteString)] -> Basepair -> Basepair
+fixSeqpos cs bp@Basepair{..} = bp{seqpos1 = seqpos1 - cl M.! chain1, seqpos2 = seqpos2 - cl M.! chain2} where
+  cl = M.fromList . snd . L.mapAccumL f 0 $ cs
+  f acc x = (acc + BS.length (snd x), (fst x, acc))
+-}
+
 -- | Helper function turning a bytestring line into a basepair entry
 
 bs2basepair :: ByteString -> Basepair
@@ -49,11 +62,11 @@
     , nucleotide1 = BS.head $ ws!!2
     , pdbnumber1  = maybe (-1) fst . readInt $ ws!!3
     , chain1      = ws!!4
-    , seqpos1     = maybe (-1) fst . readInt $ ws!!5
+    , seqpos1     = maybe (-1) (subtract 1 . fst) . readInt $ ws!!5
     , nucleotide2 = BS.head $ ws!!6
     , pdbnumber2  = maybe (-1) fst . readInt $ ws!!7
     , chain2      = ws!!8
-    , seqpos2     = maybe (-1) fst . readInt $ ws!!9
+    , seqpos2     = maybe (-1) (subtract 1 . fst) . readInt $ ws!!9
     }
   where ws = BS.words s
 
diff --git a/BiobaseFR3D.cabal b/BiobaseFR3D.cabal
--- a/BiobaseFR3D.cabal
+++ b/BiobaseFR3D.cabal
@@ -1,5 +1,5 @@
 name:           BiobaseFR3D
-version:        0.1.3.0
+version:        0.2.2.0
 author:         Christian Hoener zu Siederdissen
 maintainer:     choener@tbi.univie.ac.at
 homepage:       http://www.tbi.univie.ac.at/~choener/
@@ -23,6 +23,14 @@
                 in RNA 3D Structures, Michael Sarver; Craig L. Zirbel; Jesse
                 Stombaugh; Ali Mokdad; Neocles B. Leontis. /Journal of
                 Mathematical Biology/ (2008) 56:215–252.
+                .
+                Changes since any 0.1.*:
+                .
+                * Zero-based indexing (FR3D is one-based!) for sequence
+                  positions. We do not change the nucleotide PDB number.
+                .
+                * Some sanity checks, a number of FR3D files fall through at
+                  this and need to be checked for consistency
 
 
 
@@ -32,9 +40,10 @@
   build-depends:
     base >3 && <5,
     bytestring,
+    containers,
     filemanip,
     iteratee,
-    BiobaseXNA >= 0.5.4
+    BiobaseXNA >= 0.5.5
 
   exposed-modules:
     Biobase.FR3D