phenix.pdbtools: tools for PDB file manipulations

Purpose

phenix.pdbtools is a command line tool to perform simple maipulations on a structure in PDB file such as:

• shaking of coordinates (adding a random shift to coordinates)
• rotation-translation shift of coordinates
• shaking of occupancies
• shaking of ADP
• shifting of ADP (adding a constant value)
• scaling of ADP (multiplying by a constant value)
• setting a value to ADP
• converting to isotropic
• converting to anisotropic
• removing selected part of a model

All operations above can be performed on a whole model or any selected part.

How to run

phenix.pdbtools is run from the command line:

% phenix.pdbtools [options] [pdb_file] [parameter_file]

To get information about command line options type:

% phenix.pdbtools

To see all default parameters:

% phenix.pdbtools --show-defaults=all