[Biojava-l] Re: strange pdb

Thu Jan 12 07:52:05 EST 2006

(wow... stupid linewrap...)It seems to me, that we need a variance tag for the Group or Atom object...As a beginning... The altloc is supposedly means variation of the atomsposition, but it seems to me, it makes more sense to treat the alternates asalternative groups, as in the cases I've so far seen, these altlocs reallyrefer to alternative sidechain conformations. In this case there would be aTYR A and TYR B conformation.
On 1/12/06, Tamas Horvath <hotafin at gmail.com> wrote:>> Hi!> I've just stubled upon a strange pdb parsing fenomenon. Look at the> following pdb file:> ATOM      1  N   GLU   326      14.783  14.947 -11.793  1.00 46.17> N> ATOM      2  CA  GLU   326      15.471  16.220 -11.447  1.00 39.29> C> ATOM      3  C   GLU   326      14.978  16.646 -10.075  1.00 37.04> C> ATOM      4  O   GLU   326      13.774  16.707  -9.841   1.00 37.72> O> ATOM      5  CB  GLU   326      15.133  17.290 -12.489  1.00 45.78> C> ATOM      6  CG  GLU   326      16.102  18.482 -12.553  1.00 71.24> C> ATOM      7  CD  GLU   326      15.940  19.327 -13.826  1.00 93.39> C> ATOM      8  OE1 GLU   326      14.901  19.198 -14.512  1.00101.02> O> ATOM      9  OE2 GLU   326      16.857  20.119 -14.144  1.00 84.50> O> ATOM     10  N   TYR   327      15.913  16.885  -9.163  1.00 33.93> N> ATOM     11  CA  TYR   327      15.604  17.298  -7.797  1.00 23.92> C> ATOM     12  C   TYR   327      15.865  18.786  -7.632  1.00 24.48> C> ATOM     13  O   TYR   327      16.797  19.328  -8.230  1.00 31.71> O> ATOM     14  CB ATYR   327      16.402  16.443  -6.818  0.50 29.56> C> ATOM     15  CB BTYR   327      16.528  16.583  -6.799  0.50 30.30> C> ATOM     16  CG ATYR   327      16.280  14.990  -7.206  0.50 45.39> C> ATOM     17  CG BTYR   327      15.997  15.310  -6.184  0.50 31.62> C> ATOM     18  CD1ATYR   327      16.886  14.518  -8.371  0.50 44.19> C> ATOM     19  CD1BTYR   327      14.840  15.316  -5.413  0.50 41.31> C> ATOM     20  CD2ATYR   327      15.466  14.119  -6.496  0.50 38.02> C> ATOM     21  CD2BTYR   327      16.667  14.101  -6.351  0.50 54.42> C> ATOM     22  CE1ATYR   327      16.676  13.240  -8.828  0.50 27.11> C> ATOM     23  CE1BTYR   327      14.361  14.153  -4.823  0.50 24.22> C> ATOM     24  CE2ATYR   327      15.256  12.830  -6.944  0.50 27.50> C> ATOM     25  CE2BTYR   327      16.196  12.934  -5.764  0.50 45.82> C> ATOM     26  CZ ATYR   327      15.866  12.400  -8.119  0.50 24.52> C> ATOM     27  CZ BTYR   327      15.041  12.970  -5.001  0.50 38.12> C> ATOM     28  OH ATYR   327      15.666  11.127  -8.607  0.50 51.23> O> ATOM     29  OH BTYR   327      14.567  11.824  -4.411  0.50 40.14> O> ATOM     30  N   PHE   328      15.050  19.446  -6.825  1.00 20.97> N> ATOM     31  CA  PHE   328      15.212  20.876  -6.587  1.00 20.04> C> ATOM     32  C   PHE   328      15.213  21.072  -5.098  1.00 28.28> C> ATOM     33  O   PHE   328      14.775  20.197  -4.363  1.00 24.43> O> ATOM     34  CB  PHE   328      14.061  21.656  -7.209  1.00 22.08> C> ATOM     35  CG  PHE   328      13.906  21.406  -8.670  1.00 31.12> C> ATOM     36  CD1 PHE   328      13.164  20.320  -9.124  1.00 23.58> C> ATOM     37  CD2 PHE   328      14.547   22.217  -9.594  1.00 47.00> C> ATOM     38  CE1 PHE   328      13.064  20.044 -10.465  1.00 30.40> C> ATOM     39  CE2 PHE   328      14.452  21.948 -10.954  1.00 44.64> C> ATOM     40  CZ  PHE   328      13.706  20.852 -11.386  1.00 33.12> C>> As the pdb parser goes through these it simply cuts off those A/B variants> of that TYR, and simply just parses them as similarly named atoms of the> same 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...>>