structure_reliability Command Help

Command: $SCHRODINGER/utilities/structure_reliability

usage: structure_reliability    $SCHRODINGER/utilities/structure_reliability [<options>] <structure file>

    Structural Metric Thresholds:
    Steric Clash tolerance - 0.50/1.00(HB) Angstrom
    Bond Length Deviation  - 0.25 Angstrom
    Bond Angle Deviation   - 10.0 degree
    Dihedrals              - disallowed region
    B Factors              - outside 0-100
    Peptide Planarity      - 20.0 degree
    Sidechain Planarity    - 0.5 RMSD
    Improper Torsion       - 10.0 degree
    PDB Resolution         - 2.5
    Default Ligand RSCC    - 0.8

positional arguments:
  infile                Input Structure File

options:
  -h, --help            show this help message and exit
  -version              show program's version number and exit
  -jobname JOBNAME      Specify a non-default jobname.
  -sf SF                Specify the diffraction data file. Default is none
  -auto_detect_ligand   Automatically identify the ligand in the input file.
  -permissive_auto_detect_ligand
                        Include common non-ligand small molecules as ligands
  -ligand_name LIGAND_NAME
                        Specify the ligand by 3 letter residue name.
  -ligand_ID LIGAND_ID  Specify the ligand by chain and residue number with
                        optional insertion code like "A:38" or "A:38.C".
  -ligand_asl LIGAND_ASL
                        Specify the ligand by ASL. Comma's (,) are not
                        supported.
  -site_radius SITE_RADIUS
                        The distance cutoff for the binding site around the
                        ligand
  -site_asl SITE_ASL    Define the binding site by ASL
  -rscc RSCC            Set Real Space Correlation Coefficient threshold
                        value.
  -show                 Show the bubble plot in the terminal
  -report               Write out the text report and image (PDF)
  -chain CHAIN          Load and check one of the chains. By default all
                        chains are checked
  -get_pdbid GET_PDBID  Get the structure and diffraction data by downloading
                        from PDB website

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -WAIT                 Do not return a prompt until the job completes.
  -LOCAL                Do not use a temporary directory for job files. Keep
                        files in the current directory.
  -D, -DEBUG            Show details of Job Control operation.
  -NOJOBID              Run the job directly, without Job Control layer.