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3D-comp - Structure/Sequence Alignment to Superposition

3D-comp is intended for superposing tertiary structures of two proteins basing on alignment of their primary sequences.

Input data:
PDB file with the structure of protein 1;
PDB file with the structure of protein 2; and
Alignment of these protein sequences.

Output data:
PDB file with superposed structures;
RMSD of C-alpha atoms; and
Location parameters and rotation matrix.

Algorithm:
The method of best superposition of spatial structures independent of their initial positions in the space (Kabsch, 1976) was realized.
Location parameters and rotation matrix are calculated according to C-alpha atoms.

Reference:
Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst. 1976; A32: 922-923.

Output example:

HEADER    PROTEIN STRUCTURE ALIGNMENT	
COMPND    (A) file1 chain A (B) file2 chain B
REMARK   1
REMARK   1 Transformation of chain A coordinates:
REMARK   1 Anew = U*(Aold-shift1)+shift2
REMARK   1 The rotation matrix U:
REMARK   1       0.2843  0.9037  0.3184 
REMARK   1      -0.3886 -0.1940  0.9003 
REMARK   1       0.8767 -0.3809  0.2969 
REMARK   1      
REMARK   1 shift1 (X, Y, Z) = ( 24.434,   9.342,   8.358)
REMARK   1 shift2 (X, Y, Z) = ( 25.967,  64.677,  13.625)
REMARK   1      
REMARK   1 RMSD on Ca-atoms:  3.684 angstrom
REMARK   1      
ATOM      1  N   MET A   1      38.730  55.215  -3.247  1.00  0.00
ATOM      2  CA  MET A   1      38.092  55.938  -2.140  1.00  0.00
ATOM      3  C   MET A   1      36.924  56.821  -2.592  1.00  0.00
ATOM      4  O   MET A   1      37.119  57.872  -3.206  1.00  0.00
ATOM      5  CB  MET A   1      39.133  56.786  -1.392  1.00  0.00
ATOM      6  CG  MET A   1      38.587  57.621  -0.216  1.00  0.00
ATOM      7  SD  MET A   1      37.784  56.643   1.092  1.00  0.00
ATOM      8  CE  MET A   1      39.147  56.452   2.275  1.00  0.00
ATOM      9  N   GLN A   2      35.708  56.384  -2.279  1.00  0.00
ATOM     10  CA  GLN A   2      34.509  57.134  -2.635  1.00  0.00
ATOM     11  C   GLN A   2      33.808  57.700  -1.397  1.00  0.00
ATOM     12  O   GLN A   2      34.004  57.211  -0.285  1.00  0.00
ATOM     13  CB  GLN A   2      33.546  56.247  -3.414  1.00  0.00
ATOM     14  CG  GLN A   2      34.062  55.820  -4.780  1.00  0.00
ATOM     15  CD  GLN A   2      33.012  55.077  -5.594  1.00  0.00
ATOM     16  OE1 GLN A   2      31.804  55.288  -5.421  1.00  0.00
ATOM     17  NE2 GLN A   2      33.468  54.204  -6.493  1.00  0.00
ATOM     18  N   THR A   3      32.998  58.738  -1.593  1.00  0.00
ATOM     19  CA  THR A   3      32.277  59.357  -0.488  1.00  0.00
ATOM     20  C   THR A   3      30.778  59.069  -0.511  1.00  0.00
ATOM     21  O   THR A   3      30.168  58.918  -1.578  1.00  0.00
ATOM     22  CB  THR A   3      32.488  60.881  -0.457  1.00  0.00
ATOM     23  OG1 THR A   3      33.891  61.165  -0.440  1.00  0.00
ATOM     24  CG2 THR A   3      31.844  61.495   0.797  1.00  0.00
ATOM     25  N   ILE A   4      30.215  58.923   0.686  1.00  0.00
ATOM     26  CA  ILE A   4      28.785  58.693   0.871  1.00  0.00
ATOM     27  C   ILE A   4      28.292  59.883   1.697  1.00  0.00
ATOM     28  O   ILE A   4      28.614  59.996   2.881  1.00  0.00
ATOM     29  CB  ILE A   4      28.490  57.386   1.652  1.00  0.00
      ..
ATOM   2962  CB  LEU B 385       7.514  70.764 -17.815  1.00  0.00
ATOM   2963  CG  LEU B 385       7.267  70.676 -16.308  1.00  0.00
ATOM   2964  CD1 LEU B 385       6.707  71.973 -15.753  1.00  0.00
ATOM   2965  CD2 LEU B 385       6.317  69.529 -15.982  1.00  0.00
ATOM   2966  N   SER B 386       9.587  69.697 -20.509  1.00  0.00
ATOM   2967  CA  SER B 386       9.716  69.739 -21.951  1.00  0.00
ATOM   2968  C   SER B 386      10.554  70.875 -22.532  1.00  0.00
ATOM   2969  O   SER B 386      10.781  71.899 -21.850  1.00  0.00
ATOM   2970  OXT SER B 386      10.967  70.744 -23.728  1.00  0.00