ATOM lines in PDB files

column            1         2         3         4         5         6         7         8
number   12345678901234567890123456789012345678901234567890123456789012345678901234567890

         ATOM      1  N   GLY A   3      17.119   0.186  36.320  1.00 64.10           N  
         ATOM      2  CA  GLY A   3      16.944  -0.800  35.208  1.00 63.46           C  
         ATOM      3  C   GLY A   3      16.818  -0.087  33.851  1.00 61.22           C  
         ATOM      4  O   GLY A   3      15.721   0.337  33.463  1.00 62.81           O  
         ATOM      5  N   PRO A   4      17.944   0.077  33.129  1.00 57.39           N  
         ATOM      6  CA  PRO A   4      17.950   0.742  31.815  1.00 53.27           C  
         ATOM      7  C   PRO A   4      18.005  -0.247  30.629  1.00 49.78           C  
         ATOM      8  O   PRO A   4      19.086  -0.678  30.218  1.00 48.17           O  
         ATOM      9  CB  PRO A   4      19.191   1.613  31.898  1.00 54.33           C  
         ATOM     10  CG  PRO A   4      20.161   0.686  32.625  1.00 55.45           C  
         ATOM     11  CD  PRO A   4      19.305   0.019  33.701  1.00 55.83           C  

field id   1     2     3 4 5  6  7 8       9      10      11     12    13            1415
field id definition length format range string slicing (Python)
1 "ATOM " or "HETATM" 6 {:6s} 01-06 [0:6]
2 atom serial number 5 {:5d} 07-11 [6:11]
3 atom name 4 {:^4s} 13-16 [12:16]
4 alternate location indicator 1 {:1s} 17 [16:17]
5 residue name 3 {:3s} 18-20 [17:20]
6 chain identifier 1 {:1s} 22 [21:22]
7 residue sequence number 4 {:4d} 23-26 [22:26]
8 code for insertion of residues 1 {:1s} 27 [26:27]
9 orthogonal coordinates for X (in Angstroms) 8 {:8.3f} 31-38 [30:38]
10 orthogonal coordinates for Y (in Angstroms) 8 {:8.3f} 39-46 [38:46]
11 orthogonal coordinates for Z (in Angstroms) 8 {:8.3f} 47-54 [46:54]
12 occupancy 6 {:6.2f} 55-60 [54:60]
13 temperature factor 6 {:6.2f} 61-66 [60:66]
14 element symbol 2 {:>2s} 77-78 [76:78]
15 charge on the atom 2 {:2s} 79-80 [78:80]



Formated string for ATOM lines in PDB files (copy and paste this line into your Python code):

"{:6s}{:5d} {:^4s}{:1s}{:3s} {:1s}{:4d}{:1s}   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}          {:>2s}{:2s}".format(...)

The table above should be compliant with the PDB File Format as described in the Contents Guide Version 3.3 (Nov. 21, 2012)



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