lepingkyxk/parse_pdb_header

A Python 3 script for parsing the header information of PDB files, such as Experiment Method, Resolution, R_free value and mean B-factor

Descriptions of the parse_PDB_header

A Python 3 script for parsing the header information of PDB files.

The main purpose of this script is to extract some of the header information, such as Experiment Method, Resolution, R value, R_free value, mean B-factor, then calculate the grades of Resolution and R_free value based on the grading of FirstGlance in Jmol. Finally, saving above mentioned information as a .csv file (Pandas DataFrame).

Note: In some PDB files (due to the complex of the protein's structure and the limitations of the experimental detections), the R value have different data, even in the same PDB file, or shown as NULL. Similarly for the R_free value. In addition, the mean B-factor some times reported as NULL

For examples:

In 1BRT.pdb,

REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.140                           
REMARK   3   R VALUE            (WORKING SET) : 0.147                         
REMARK   3   FREE R VALUE                     : 0.164                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 2283                            

In 1GPD.pbd

REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : NULL                            
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL                            
REMARK   3   R VALUE            (WORKING SET) : NULL                            
REMARK   3   FREE R VALUE                     : NULL                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL   
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL                            
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL     
...
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                         
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 

Usage

For example

python parse_PDB_header.py

Then the program will ask you to input the directory that contains the PDB files.

>>> Please type the directory contains PDB files:

If you are already in that directory, you only need to type ./ as input.

Acknowledgements

I thank Wayne for discussion about the calc_R_free_grade() and deal_round() functions. I also would like to thank Zachary Ware for the detailed of the Decimal() function, which published on 2015-08-08 09:36.