How to read pdb files
1
0
Entering edit mode
6 weeks ago
jiyecec574 • 0

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

Pdb python • 187 views
ADD COMMENT
3
Entering edit mode
6 weeks ago
Mensur Dlakic ★ 15k

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
ADD COMMENT

Login before adding your answer.

Traffic: 2390 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6