PDBCOP is a command line based tool which assembles specific details about your X-ray structure model from a PDB file. This tool can:
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Print list of non standard residues in PDB file
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Print minimum, maximum, and average B factor values in chains and for the whole structure
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List all atoms with occupancy close to 0
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List all atoms with occupancy different from 0.00 and 1.00
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List all residues with alternate conformations
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Output sequence of protein chains in fasta format
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Compare two PDB files - usually before and after refinement - and print out otoms that differ in position and B factor more than a certain threshold
PDBCOP can be run from command line under Linux.
How to Run:
pdbcop [-l] [-d] [-s] file1 (file2) [shift_tol] [delta_B_tol]
-l
long list: lists all atoms with occupancy different from 0.00 and 1.00
-s
prints out sequence
-d
compares atom positions and B-factors in two PDB files
shift_tol
minimal shift to be printed, default value: 0.2
delta_B_tol
minimal difference in B to be printed, default value: 3.5
(Alternate locations, occupancies and B-factors are printed only for the first file.)
Examples:
pdbcop file1.pdb
pdbcop -ls file1.pdb
pdbcop -d 1.pdb 2.pdb Example of output
pdbcop -dl 1.pdb 2.pdb 0.3 5
News:
August 18 2015: bug fixes, check of anisotropic ADP's
July 13 2015: bug fixes