phenix.pdbtools: tools for PDB file manipulations

List of all pdbtools keywords

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

List of all pdbtools keywords

------------------------------------------------------------------------------- 
Legend: black bold - scope names
        black - parameter names
        red - parameter values
        blue - parameter help
        blue bold - scope help
        Parameter values:
          * means selected parameter (where multiple choices are available)
          False is No
          True is Yes
          None means not provided, not predefined, or left up to the program
          "%3d" is a Python style formatting descriptor
------------------------------------------------------------------------------- 
selection= None Selection for atoms to be modified
adp Scope of options to modify ADP of selected atoms
   randomize= None Randomize ADP within a certain range
   set_b_iso= None Set ADP of atoms to set_b_iso
   convert_to_isotropic= None Convert atoms to isotropic
   convert_to_anisotropic= None Convert atoms to anisotropic
   shift_b_iso= None Add shift_b_iso value to ADP
   scale_adp= None Multiply ADP by scale_adp
sites Scope of options to modify coordinates of selected atoms
   shake= None Randomize coordinates with mean error value equal to shake
   translate= 0 0 0 Translational shift
   rotate= 0 0 0 Rotational shift
   euler_angle_convention= *xyz zyz Euler angles convention to be used for
                           rotation
occupancies Scope of options to modify occupancies of selected atoms
   randomize= None Randomize occupancies within a certain range
output Write out PDB file with modified model (file name is defined in
       write_modified)
   pdb
      file_name= None
remove
   selection= None Select atoms to be removed
input
   pdb
      file_name= None Model file(s) name (PDB)
   crystal_symmetry Unit cell and space group parameters
      unit_cell= None
      space_group= None