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[back to overview]

B-factor statistics

Script to calculate B-factor statistics of a PDB file.

Usage

Run ./pdb_bfactor_stats.py for more usage information.

usage: pdb_bfactor_stats.py [-h] [-i INPUT] [-p] [-l] [-a ATOMS]

Calculates B-factor statistics of PDB file

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input PDB file.
  -p, --protein         includes ATOM residues.
  -l, --ligand          includes HETATM residues.
  -a ATOMS, --atoms ATOMS
                        options: all, mainchain, calpha


Example 1

  • B-factor statistics of all protein atoms.

Input:

./pdb_bfactor_stats.py --input ~/Desktop/1RX1.pdb --protein

Screen Output:

Median B-factor: 14.58
Average B-factor: 19.951
Standard Deviation: 16.577
Standard Error: 0.466
Number of B-factors: 1268


Example 2

  • B-factor of main-chain atoms only.

Input: ./pdb_bfactor_stats.py --input ~/Desktop/1RX1.pdb --protein --atoms mainchain

Screen Output:

Median B-factor: 12.975
Average B-factor: 15.906
Standard Deviation: 11.089
Standard Error: 0.44
Number of B-factors: 636