Author(s)

• superpose_and_morph: Tom Terwilliger

Purpose

Superpose moving model on fixed model, then optionally morph the moving model to be similar to the fixed model and trim it back to the parts that match.

Usage

How superpose_and_morph works:

superpose_and_morph uses a combination of sequence-based and SSM-based (secondary structure matching) to superimpose two models. The sequence-based matching is the same as in phenix.superpose_pdbs. The SSM matching is the same as in phenix.search_and_morph. The SSM matching consists of identifying secondary structure in the two models, indexing all pairs of secondary structure elements, and finding sets of matching pairs in the two structures. Normally the basic unit of a match is a set of three pairs of secondary structure elements (they can be overlapping) with the same spatial arrangement in the two structures. Such a match is called a triple in superpose_and_morph.

A matching triples yields a unique orientation of the moving model. Matching triples are grouped into sets in which all the triples yield nearly the same orientation. Then the transformations suggested by the largest groups are each tested by using them to superimpose the moving model on the fixed model and noting the number of residues that superimpose.

The best-fitting superimposed moving models are then (optionally) morphed by calculation of a real-space distortion field that changes over a typical distance of about 10 A (set by the parameter distortion_field_length).

Finally (optionally) the moving models are trimmed to remove segments that are very different from the fixed model.

Examples

Standard run of superpose_and_morph:

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

phenix.superpose_and_morph fixed_model=fixed_model.pdb \
   moving_model=moving_model.pdb

This will superimpose moving_model.pdb on fixed_model.pdb, morph it (gradual adjustment of atomic positions with location along the chain and in space), and trim moving_model back to the region where they are similar.

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all available keywords

• job_title = None Job title in PHENIX GUI, not used on command line
• input_files
  • fixed_model = None Input fixed PDB file
  • fixed_selection = None If specified, only include selected part of fixed model
  • moving_model = None Input moving PDB file. Model to superpose on fixed_model
  • moving_selection = None If specified, only include selected part of moving model
• output_files
  • superposed_model = None Output file with superposed moving model
• superpose_and_morph
  • superpose = True Superpose moving model on fixed model
  • morph = True Morph moving model after superposition
  • trim = True Trim moving model after morphing
  • shift_field_distance = None Shift field distance. Distance over which morphing leaves model mostly the same. Over longer distances morphing changes model. Default is 10 A.
  • good_enough_fraction = 0.9 Good enough fraction. If this much of model is found with sequence-based search skip ssm
  • starting_distance_cutoff = 2.5 Starting distance cutoff. Try to keep atoms within this distance, but increase if too few are found.
  • include_ssm = True Include ssm matching
  • include_lsq = True Include lsq matching
  • try_lsq_first = True Try lsq matching first if lsq and ssm are both included
  • try_with_fragments_if_poor_fit = True Try lsq matching with fragments if no fit obtained
  • include_swapped_match = None Try matching fixed to moving if initial match fails
  • allow_reverse_connectivity = None Allow match to reversed model
  • direct_morph = False Directly morph moving model onto fixed model. Requires chain ID and residue numbering to be identical, but fixed_model can have missing residues. Does not allow trimming.
• control
  • nproc = 1 Number of processors to use. If None, uses all available
• guiGUI-specific parameter required for output directory
  • output_dir = None