How to read pdb files

Question

[jiyecec574]

How can you determine or find phosphate atoms of the dna in a pdb file format ?

Answer 1

[Mensur Dlakic]

Most of the time lines in PDB files have the atom type stored in two spots: in columns 14-16 and in 78-endofline. So this would be a phosphate atom:

ATOM     42  P    DT B 303     -16.004  54.386   0.278  1.00 30.13           P

These two would not be phosphates even though they have a P in columns 14-16. They are oxygens that are attached to phosphates, which you can see because the atom at the end is O.

ATOM     43  OP1  DT B 303     -15.477  54.884   1.543  1.00 36.17           O
ATOM     44  OP2  DT B 303     -15.689  55.173  -0.904  1.00 32.13           O