Author(s)

• search_and_morph: Tom Terwilliger

Purpose

Search for structures in the PDB similar to a supplied model using SSM matching, superimpose the matching structures, then optionally morph them to be similar to the target model and trim back to the parts that match.

Usage

How search_and_morph works:

search_and_morph uses SSM-based (secondary structure matching) to find structures in the PDB that are similar to a supplied model. The SSM matching is the same as in phenix.superpose_and_morph. The SSM matching starts with identifying secondary structure in the supplied model, indexing all pairs of secondary structure elements. These pairs of secondary structure elements are compared with indexed pairs from all structures in a curated subset of the PDB, leading to sets of matching pairs in the target and structures in the PDB.

The curated subset of the PDB consist of non-redundant (<90% identity), high-resolution structures (< 2 A) that have very good geometry. The main-chain coordinates of these structures are supplied in a database as part of Phenix.

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 search_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. The PDB entries representing the largest groups are then tested for match to the target structure.

Optionally (if database is set to "pdb100"), sequence neighbors of these PDB entries are identified and added to the structures tested for matching the target structure

The structures to be examined are either loaded from the Phenix database or downloaded from the PDB. They are then superimposed on the target structure and (optionally) morphed and trimmed to match the target structure in the same way as in phenix.superimpose_and_morph. In this procedure the best-fitting superimposed structures are 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 search_and_morph:

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

phenix.search_and_morph model.pdb nproc=8

This will find structures in the PDB similar to model.pdb, superimpose them, morph them to match, and trim back to the matching region.

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
  • model = None Input PDB file to try and match
  • selection = None If specified, only include selected part of model
  • local_pdb_dir = None Local PDB mirror (something like /User/files/pdb_mirror/)
• output_files
  • superposed_model_prefix = None Output files with superposed models will begin with this prefix
• search_and_morph
  • morph = True Morph moving model after superposition
  • trim = True Trim moving model after morphing
  • replace_structure_elements = True Replace each secondary structure element (helices/strands) with idealized version before finding matching segments in PDB. Includes replacing individual strands with helices if spacing from other secondary structure is suitable and density is compatible with a helix.
  • database = *pdb100 pdb2018_90 Database to search. pdb100 is unique set of PDB. pdb2018_90 is quality-filtered PDB at 90% identity
  • number_of_sequence_neighbors = None Number of sequence neighbors to search if using pdb100. Default is 10 for quick, 100 otherwise
  • max_models = 1 Number of models to return
  • allow_reverse_connectivity = False Allow match to reversed model
  • pdb_include_list = None List of PDB ID or pdb ID and chain_id to include ( e.g., 2DY1 or 2DY1_A)
  • pdb_exclude_list = None List of PDB ID or pdb ID and chain_id to exclude (2DY1 or 2DY1_A)
  • exclude_similar_to_this_pdb_id = None Exclude all PDB chains with sequence identity > maximum_percent_identity_to_this_pdb_id to exclude_similar_to_this_pdb_id
  • maximum_percent_identity_to_this_pdb_id = 30 Maximum percent identity to supplied PDB chain to include. Exclude all PDB chains with sequence identity > maximum_percent_identity_to_this_pdb_id to exclude_similar_to_this_pdb_id
  • max_models_to_fetch = None Maximum number of models to fetch from PDB. Default is 10 for quick and 100 otherwise
  • starting_distance_cutoff = 2.5 Starting distance cutoff. Try to keep atoms within this distance, but increase if too few are found.
  • 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.
• control
  • nproc = 1 Number of processors to use. If None, uses all available
  • quick = False Run quickly
• guiGUI-specific parameter required for output directory
  • output_dir = None