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

Parameters can be changed from the command line:

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 available keywords

• 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 " " or altloc "A")' 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 " " or altloc "A")' 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
  • pdb_file_name_moving_other = None Name of another PDB file to transform with the same matrix as pdb_file_name_moving
• output
  • file_name = None Name of PDB file with model that best fits to pdb_file_name_fixed
  • overwrite = True Overwrite existing files
  • target_output_format = *None pdb mmcif Desired output format (if possible). Choices are None ( try to use input format), pdb, mmcif. If output model does not fit in pdb format, mmcif will be used. Default is pdb.
  • job_title = None Job title in PHENIX GUI, not used on command line
• alignmentSet 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