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Cleanup alternate locations for residues in a PDB file (Informatics)

This tool runs the pdb_selaltloc function from pdb-tools python package to clean up alternate locations for residues in a PDB file.

Input

  • pdb_file: File path to a PDB file that contains alternate locations for residues
  • select_certain_altloc: when provided, only the residues with the specified alternate location will be kept in the output file. Otherwise, the alternate location with the highest occupancy will be kept.

Output

A cleaned PDB file with only one location for each residue

Citation

Rodrigues JPGLM, Teixeira JMC, Trellet M and Bonvin AMJJ. pdb-tools: a swiss army knife for molecular structures. F1000Research 2018, 7:1961 (https://doi.org/10.12688/f1000research.17456.1)