geometry_pdbtools
This script provides multiple functions for work with pdb files. They are selected by commandline option.
Update geometry from .xyz file
Option -x or --xyz
Update geometry of PDB file with geometry in .xyz format.
Convert segment information to chain
Option -c or --chain-from-seg
Some PDB files use segment information instead of chain record to specify parts of the system, but this notation does not comply to the PDB standard. This option converts the segment to chain, taking first letter of the segment name as the name of the chain.
Print sequence
Option -s or --sequence
Prints sequence of residues in the PDB file. In addition to use of the original residue names, the sequence of a protein is translated to the one letter code.
In the short notation, waters are written as '~' and unknown residues as '.'.
Print list of residues
Option -r or --residue-summary
Prints list of residues, including chain information, residue name and residue number.