Molprobity API

The Molprobity API takes as input a PDB file and runs MolProbity with the default settings, returning an HTML report. This tool is useful for identifying issues with atomic detail level models (See Notes for more information).

Command Line Interface

Examples

Submit a job

lev engine submit molprobity input.pdb

Flags

  • --pdb-file (str) (Required)
    • Input PDB to evaluate in MolProbity

Python Interface

Examples

Submit a job

from engine import EngineClient

client = EngineClient()
client.authorize()

job_id = client.submit_molprobity(
    pdb_path="input.pdb"
)

Flags

  • pdb_path (str) (Required)
    • Input PDB to evaluate in MolProbity

Outputs

  • report.tgz
    • HTML MolProbity report

Notes

  • MolProbity is a structure-validation web service that diagnoses and evaluates model quality at global and local levels
    • Analyses performed by MolProbity include:
      • Addition of H atoms
      • All-atom contact analysis
      • Torsion-angle combinations
      • Covalent-geometry analyses
      • Nucleic acid analyses
    • Provides an overall MolProbity score based on a combination of the analyses conducted listed above.
  • See References for additional resources and information on MolProbity

References

MolProbity: all-atom structure validation for macromolecular crystallography

MolProbity

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