Output Files

PDB Output :

The configurations are saved in the PDB Format. Each configuration as a different model, like in NMR-PDB files. The residue number (column #5) is the Label number from the Positions File (*.pos). The Occupancy and the Temperature Factor (columns #9 and #10) containing both a value, which corresponds to the minimization energy. The larger this value, the worse is the consistency of the FRET distances. This value can be visualized e.g. by using the "Colour:Temperature"-option in RasMol.

sample.pdb :

     MODEL       1

     ATOM      1  C   LYS   10     -5.114   6.164   1.437  0.00  0.00        A

     ATOM      2  C   LYS    20      5.284   6.497  -3.400   0.00  0.00        A

     ATOM      3  C   LYS    30      3.489   3.949   6.307   0.00  0.00        A

     ATOM      4  C   LYS    40     -2.899 -16.720  -6.218  0.00  0.00        A

     ATOM      5  C   LYS    50     3.684   45.852   4.307   0.00  0.00        A

     ENDMDL

     MODEL       2

     ATOM      1  C   LYS   10     -4.821   5.944   0.249   0.00  0.00        A

     ATOM      2  C   LYS    20      4.772   7.085  -3.916   0.00  0.00        A

     ATOM      3  C   LYS    30      2.497   4.166   7.511   0.00  0.00        A

     ATOM      4  C   LYS    40      0.553 -17.91   -0.313   0.00  0.00        A

     ATOM      5  C   LYS    50     -2.601  44.442 10.049   0.00  0.00        A

     ENDMDL

     MODEL       3

     ATOM      1  C   LYS   10     -4.575   6.339    0.660   0.00  0.00        A

     ATOM      2  C   LYS    20      3.998   6.439  -3.193   0.00  0.00        A

     ATOM      3  C   LYS    30      2.643   5.117   5.905   0.00  0.00        A

     ATOM      4  C   LYS    40     -2.561 -17.524 -0.644   0.00  0.00        A

     ATOM      5  C   LYS    50      3.761  45.263   4.512   0.00  0.00        A

     ENDMDL

     MODEL       4

     ATOM      1  C   LYS   10     -5.248   6.910    1.384   0.00  0.00        A

     ATOM      2  C   LYS    20      3.487   6.726   -3.466   0.00  0.00        A

     ATOM      3  C   LYS    30      3.537   4.536    5.724   0.00  0.00        A

     ATOM      4  C   LYS    40     -1.294 -17.529 -2.996   0.00  0.00        A

     ATOM      5  C   LYS    50      4.766  45.728   2.837   0.00  0.00        A

     ENDMDL

     ...

Povray Input :

FRETsg writes a Povray input file (*.pov), if the corresponding flag is set in the Parameter File (*.inp). For each label a Blob object is defined, that contains the positions from all configurations. The choice of values in the camera section is not very intelligent, you have to adjust them manually. For more information please visit the official Povray Homepage.

   To use the generated input with povray, try:

     #>  povray +Isample.pov +H300 +W300