Overview

Structure_search is a tool to quickly identify structural homologs of the input PDB file from the Protein Data Bank. It uses the SARST algorithm, and it's very fast. A typical search time against the whole PDB is usually less than one second. There is an option to allow users to obtain a list of ligands found in structures of those homologs.

Usage

• obtain a list of PDB ids and chains sorted by similarities to mypdb.pdb

  phenix.structure_search mypdb.pdb

• obtain a list of homologs of mypdb.pdb and all ligands found in structures of those homologs

  phenix.structure_search mypdb.pdb get_ligand=True

More information can be found in input/Output files sections below:

Input files

required input:

• pdb_file: the file containing the protein model of interest.

Optional inputs :

• get_ligand:"=True" if want a list of ligands found in homologous PDBs, Default = False.
• job_title: current job title
• output_prefix: prefix for output files if needed.
• get_pdb:Collect and superpose the top N omologous pdbs (default=10).
• coot_display: Display superposed pdb files in coot. (default=True)

Output files

In addition to screen output, these files contains results of structure_search:

• output.txt: file containing homologs of 'pdb_file' sorted by scores.
• pdb_ligand.txt (if get_ligand=True): file containing all ligands found in all homologs from this search.

References

Lo WC, Huang PJ, Chang CH, Lyu PC. BMC Bioinformatics. 2007, 8:307

List of all available keywords

• structure_search
  • pdb_file = None Enter a PDB file name
  • output_prefix = 'output' Provide an output prefix if needed
  • blastpath = None Enter path to blastall executable
  • get_ligand = False Use get_ligand=True to retrive ligands.
  • get_pdb = 10 get_pdb=N will collect and superpose the top N homologous pdbs. Use get_pdb=0 to disable this option.
  • coot_display = True (default) Display output pdb files in coot.
  • verbose = False verbose output
  • debug = False debugging output
  • job_title = None Job title in PHENIX GUI, not used on command line