Author(s)

• fragment_search: Tom Terwilliger

Purpose

Extract a segment from the PDB that is similar to a segment in a supplied model.

This tool can be used in early stages of model-building to try and improve a segment in a preliminary model by replacing it with a similar fragment from a deposited structure.

Note that the fragment from the PDB may not actually have good geometry because it is morphed (distorted) to match the supplied model.

Fragment search differs from replace_with_fragments_from_pdb in that fragment_search is looking for a single fragment from the PDB that matches a target segment in your model, while replace_with_fragments_from_pdb is trying to completely replace your model with a set of fragments.

Usage

fragment_search can find a fragment in the PDB similar to a supplied fragment (protein chains only)

You can adjust the maximum number of insertions/deletions in the replacement fragment and whether to morph the fragment.

You can also choose to exclude or include specific PDB entries or exclude all PDB entries with sequences similar to a particular PDB entry.

You can choose to create a replacement for just a selected part of your model (by supplying a selection string that specifies what to select).

How fragment_search works:

Fragment searching is done using a quality-filtered set of chains from the PDB, filtered at 90% sequence identity (pdb2018_90). 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.

Potential matching fragments are found by comparing end-to-end distances for the target with all fragments of the desired length in structures in the database. Fragments with the desired end-to-end distance are then examined for matching of distances from end to several internal positions in the target fragment. Finally those that match all these are superimposed on the target fragment, morphed to match the target fragment, and the rmsd of CA positions are used to evaluate the match.

Morphing includes two steps. In the first, the fragment is distorted with an offset that changes linearly for each residue along the chain and that allows the first and last CA positions of the matching fragment to superimpose on those of the target fragment.

In the second step, a distortion field is applied to the matching fragment to make it more similar to the target fragment. This morphing consists of calculation of a real-space distortion field that changes over a typical distance of about 10 A (set by the parameter distortion_field_length), and applying this distortion field to all the atoms in the matching fragment.

Examples

Standard run of fragment_search:

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

phenix.fragment_search model.pdb nproc=8 selection="chain A and resseq 1:20"

This will find fragments in the PDB similar to residues 1-20 of model.pdb.

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 with segments to try and match
  • selection = None If specified, match selected part of model
• output_files
  • superposed_model_prefix = None Output files with superposed models will begin with this prefix
• fragment_search
  • trim = True Trim models down to match the target fragment. Otherwise return full chain
  • n_res = None Number of residues to get. If None, use number of residues in input fragment
  • max_indel = 0 Maximum insertions/deletions relative to n_res
  • n_half_window = 5 Number of residues over which to average morphing shifts
  • max_gap = 20 Maximum gap in match to keep. Interpolate morphing values over gaps up to max_gap. Trim gaps longer than max_gap
  • max_segment_matching_ca_ca_deviation = 0.8 Maximum rmsd between segments to allow a match
  • max_models = 1 Number of models to return
  • morph = True Morph output models after superposition and before trimming
  • pdb_include_list = None List of PDB ID or pdb ID and chain_id to include (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
• control
  • nproc = 1 Number of processors to use. If None, uses all available
  • write_files = True Write output files
• guiGUI-specific parameter required for output directory
  • output_dir = None