[Biojava-l] strange pdb

Thu Jan 12 07:17:31 EST 2006

Hi!I've just stubled upon a strange pdb parsing fenomenon. Look at thefollowing pdb file:ATOM      1  N   GLU   326      14.783  14.947 -11.793  1.00 46.17NATOM      2  CA  GLU   326      15.471  16.220 -11.447  1.00 39.29CATOM      3  C   GLU   326      14.978  16.646 -10.075  1.00 37.04CATOM      4  O   GLU   326      13.774  16.707  -9.841  1.00 37.72OATOM      5  CB  GLU   326      15.133  17.290 -12.489  1.00 45.78CATOM      6  CG  GLU   326      16.102  18.482 -12.553  1.00 71.24CATOM      7  CD  GLU   326      15.940  19.327 -13.826  1.00 93.39CATOM      8  OE1 GLU   326      14.901  19.198 -14.512  1.00101.02OATOM      9  OE2 GLU   326      16.857  20.119 -14.144  1.00 84.50OATOM     10  N   TYR   327      15.913  16.885  -9.163  1.00 33.93NATOM     11  CA  TYR   327      15.604  17.298  -7.797  1.00 23.92CATOM     12  C   TYR   327      15.865  18.786  -7.632  1.00 24.48CATOM     13  O   TYR   327      16.797  19.328  -8.230  1.00 31.71OATOM     14  CB ATYR   327      16.402  16.443  -6.818  0.50 29.56CATOM     15  CB BTYR   327      16.528  16.583  -6.799  0.50 30.30CATOM     16  CG ATYR   327      16.280  14.990  -7.206  0.50 45.39CATOM     17  CG BTYR   327      15.997  15.310  -6.184  0.50 31.62CATOM     18  CD1ATYR   327      16.886  14.518  -8.371  0.50 44.19CATOM     19  CD1BTYR   327      14.840  15.316  -5.413  0.50 41.31CATOM     20  CD2ATYR   327      15.466  14.119  -6.496  0.50 38.02CATOM     21  CD2BTYR   327      16.667  14.101  -6.351  0.50 54.42CATOM     22  CE1ATYR   327      16.676  13.240  -8.828  0.50 27.11CATOM     23  CE1BTYR   327      14.361  14.153  -4.823  0.50 24.22CATOM     24  CE2ATYR   327      15.256  12.830  -6.944  0.50 27.50CATOM     25  CE2BTYR   327      16.196  12.934  -5.764  0.50 45.82CATOM     26  CZ ATYR   327      15.866  12.400  -8.119  0.50 24.52CATOM     27  CZ BTYR   327      15.041  12.970  -5.001  0.50 38.12CATOM     28  OH ATYR   327      15.666  11.127  -8.607  0.50 51.23OATOM     29  OH BTYR   327      14.567  11.824  -4.411  0.50 40.14OATOM     30  N   PHE   328      15.050  19.446  -6.825  1.00 20.97NATOM     31  CA  PHE   328      15.212  20.876  -6.587  1.00 20.04CATOM     32  C   PHE   328      15.213  21.072  -5.098  1.00 28.28CATOM     33  O   PHE   328      14.775  20.197  -4.363  1.00 24.43OATOM     34  CB  PHE   328      14.061  21.656  -7.209  1.00 22.08CATOM     35  CG  PHE   328      13.906  21.406  -8.670  1.00 31.12CATOM     36  CD1 PHE   328      13.164  20.320  -9.124  1.00 23.58CATOM     37  CD2 PHE   328      14.547  22.217  -9.594  1.00 47.00CATOM     38  CE1 PHE   328      13.064  20.044 -10.465  1.00 30.40CATOM     39  CE2 PHE   328      14.452  21.948 -10.954  1.00 44.64CATOM     40  CZ  PHE   328      13.706  20.852 -11.386  1.00 33.12C
As the pdb parser goes through these it simply cuts off those A/B variantsof that TYR, and simply just parses them as similarly named atoms of thesame aa. This is really not a desired thing to do.As in the pdb format description, this is:
17             Character       altLoc        Alternate location indicator.

Maybe the simplest way to deal with it is to let the user choose,which wariant should be used...