Superimposing two PDB files with superpose_pdbs

Author(s)

Purpose

Usage

How superpose_pdbs works:

Output files from superpose_pdbs

Examples

Standard run of superpose_pdbs:

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all superpose_pdbs keywords

Author(s)

• superpose_pdbs: Peter Zwart, Pavel Afonine, Ralf W. Grosse-Kunstleve

Purpose

superpose_pdbs is a command line tool for superimposing one PDB model on another and writing out the superimposed model.

Usage

How superpose_pdbs works:

superpose_pdbs performes a least-squares superposition of two selected parts from two pdb files. If no selections is provided for fixed and moving models the whole content of both input PDB files is used for superposition. If the number of atoms in fixed and moving models is different and the models contain amino-acid residues then the sequence alignment is performed and the matching residues (CA atoms by default, can be changed by the user) are used for superposition. Note that selected (and/or matching) atoms are the atoms used to find the superposition operators while these operators are applied to the whole moving structure.

Output files from superpose_pdbs

A PDB file with fitted model.

Examples

Standard run of superpose_pdbs:

Running the superpose_pdbs is easy. From the command-line you can type:

phenix.superpose_pdbs fixed.pdb moving.pdb

phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and name CA" selection_moving="chain B and name CA"

Possible Problems

Specific limitations and problems:

• Different number of atoms in selection_fixed and selection_moving in case when no sequence alignment can be performed (the molecules contain no amino-acid residues) or sequence alignment failed to find matching residues.

• More than one model in one PDB file (separated with MODEL-ENDMDL)

Literature

Additional information

List of all superpose_pdbs 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_fixed= None Selection of the target atoms to fit to (optional)
selection_moving= None Selection of the atoms that will be fit to
                  selection_fixed (optional)
selection_default_moving= pepnames and (name ca or name n or name c) and
                          'altloc " "' Select protein atoms that will be used
                          in superposition after sequence alignment
selection_default_fixed= pepnames and (name ca or name n or name c) and
                         'altloc " "' Select protein atoms that will be used
                         in superposition after sequence alignment
reciprocal_matching= False try both orientations for homodimers
input
   pdb_file_name_fixed= None Name of PDB file with model to fit to
   pdb_file_name_moving= None Name of PDB file with model that will be fit to
                         pdb_file_name_fixed
output
   file_name= None Name of PDB file with model that best fits to
              pdb_file_name_fixed
   job_title= None Job title in PHENIX GUI, not used on command line
alignment Set of parameters for sequence alignment. Defaults are good for most
          of cases
   alignment_style= local *global
   gap_opening_penalty= 1
   gap_extension_penalty= 1
   similarity_matrix= blosum50 dayhoff *identity