PDBCOP.py Documentation

History

This script is completely inspired by the program crysa.fzu.cz/pdbcop written by Karla Fejfarova.

Script Functionality

PDBCOP.py is a command line based tool which assembles specific details about your X-ray structure model from a PDB or mmCIF file. This tool can:

• Print list of non standard residues in PDB file
• Print minimum, maximum, and average B factor values in chains and for the whole structure
• List all atoms with occupancy close to 0
• List all atoms with occupancy different from 0.00 and 1.00
• List all residues with alternate conformations
• Output sequence of protein chains in fasta format
• Compare two PDB or mmCIF files - usually before and after refinement - and print out otoms that differ in position and B factor more than a certain threshold

Download

Python3

• pdbcop.py
• pdbcop_gui.py

Linux binary (using PyInstaller)

• pdbcop
• pdbcop_gui

Window binary (using PyInstaller)

• pdbcop.exe
• pdbcop_gui.exe

Help (command line)

usage: pdbcop.py [-h] [-c CIF] [-c2 CIF2] [-p PDB] [-p2 PDB2] [-v] [-s] [-dc DELTA_COORDINATES] [-da DELTA_ADP] [-l LOG]

options:
  -h, --help            show this help message and exit
  -c CIF, --cif CIF     input mmCIF file
  -c2 CIF2, --cif2 CIF2
                        second mmCIF file for comparison
  -p PDB, --pdb PDB     input PDB file
  -p2 PDB2, --pdb2 PDB2
                        second PDB file for comparison
  -v, --verbose         prints more detailed log
  -s, --sequence        prints out sequence
  -dc DELTA_COORDINATES, --delta_coordinates DELTA_COORDINATES
                        minimal shift to be reported, default 0.2
  -da DELTA_ADP, --delta_adp DELTA_ADP
                        minimal delta in ADP to be reported, default 3.5
  -l LOG, --log LOG     logfile name (default pdbcop.log)
  -v VERBOSE, --verbose VERBOSE
                        logfile verbosity, 1 = short, 2 = normal, 3 = long, default 2

Report all issues at kolenpe1 [at] cvut.cz.

Example of command line use:

python3 pdbcop.py -c file.cif -c2 file2.cif -dc 0.4 -da 5 -l my_new.log

Output Example (PDB entry 2RGS):

• 2rgs-short.log - verbosity 1
• 2rgs-medium.log - verbosity 2
• 2rgs-long.log - verbosity 3