Superimposing two PDB files with superpose_pdbs
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 " "' 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
- 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