PDB file format 2.3

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PDB file format 2.3

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format range. Python extraction. 1. 6. %-6s. 01â06. [0:6]. 2. 5. %5d. 07â11. [6:11] ... taken from http://www.wwpdb.org/documentation/format23/sect9.html#ATOM.

PDB file format 2.3 1 2 3 4 5 6 7 8 column number 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0

field

field 1 2

A T O M 1 N G L Y A

3 1 7 . 1 1 9 0 . 1 8 6 3 6 . 3 2 0 1 . 0 0 6 4 . 1 0 N

A T O M 2 C A G L Y A

3 1 6 . 9 4 4 0 . 8 0 0 3 5 . 2 0 8 1 . 0 0 6 3 . 4 6 C

A T O M 3 C G L Y A

3 1 6 . 8 1 8 0 . 0 8 7 3 3 . 8 5 1 1 . 0 0 6 1 . 2 2 C

A T O M 4 O G L Y A

3 1 5 . 7 2 1 0 . 3 3 7 3 3 . 4 6 3 1 . 0 0 6 2 . 8 1 O

A T O M 5 N P R O A

4 1 7 . 9 4 4 0 . 0 7 7 3 3 . 1 2 9 1 . 0 0 5 7 . 3 9 N

A T O M 6 C A P R O A

4 1 7 . 9 5 0 0 . 7 4 2 3 1 . 8 1 5 1 . 0 0 5 3 . 2 7 C

A T O M 7 C P R O A

4 1 8 . 0 0 5 0 . 2 4 7 3 0 . 6 2 9 1 . 0 0 4 9 . 7 8 C

A T O M 8 O P R O A

4 1 9 . 0 8 6 0 . 6 7 8 3 0 . 2 1 8 1 . 0 0 4 8 . 1 7 O

A T O M 9 C B P R O A

4 1 9 . 1 9 1 1 . 6 1 3 3 1 . 8 9 8 1 . 0 0 5 4 . 3 3 C

A T O M 1 0 C G P R O A

4 2 0 . 1 6 1 0 . 6 8 6 3 2 . 6 2 5 1 . 0 0 5 5 . 4 5 C

A T O M 1 1 C D P R O A

4 1 9 . 3 0 5 0 . 0 1 9 3 3 . 7 0 1 1 . 0 0 5 5 . 8 3 C

1

2

3

4

definition 'ATOM ' or 'HETATM' atom serial number

3 4 5

atom name alternate location indicator residue name

6 7 8

chain identifier residue sequence number code for insertion of residues

9 10 11 12 13

orthogonal coordinates for X in Angstrom orthogonal coordinates for Y in Angstrom orthogonal coordinates for Z in Angstrom occupancy temperature factor

14 15

element symbol charge on the atom

Python formated string :

5

6

length 6 5 1 4 1 3 1 1 4 1 3 8 8 8 6 6 10 2 2

7

8

9

format %-6s %5d

range 01—06 07—11

Python extraction [0:6] [6:11]

%4s %1s %3s

13—16 17 18—20

[12:16] [16:17] [17:20]

%1s %4d %1s

22 23—26 27

[21:22] [22:26] [26:27]

%8.3f %8.3f %8.3f %6.2f %6.2f

31—38 39—46 47—54 55—60 61—66

[30:38] [38:46] [46:54] [54:60] [60:66]

%2s %2s

77—78 79—80

[76:78] [78:80]

10

11

12

13

14

15

%6s%5d %4s%1s%3s %1s%4d%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2s

PDB File Format - Contents Guide Version 2.3 (July 09, 1998) reference taken from http://www.wwpdb.org/documentation/format23/sect9.html#ATOM

PP 12/01/2011