diff --git a/examples/scoring/README.md b/examples/scoring/README.md index 331776edb009c99db4099b56d61c3eef8badc197..533ce96d311f0ec2453a2657e9be35b3bfa18569 100644 --- a/examples/scoring/README.md +++ b/examples/scoring/README.md @@ -34,6 +34,8 @@ default output (out.json): ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score ``` +Example output: [compare-structures_example_out.json] + By default, model-reference chains are aligned using Needleman-Wunsch. Many benchmarking efforts such as CASP and CAMEO assume residue numbers according to target sequence(s). Both "actions" allow to derive model-reference @@ -44,12 +46,15 @@ cases. This can be enabled by adding a `-rna` (residue number alignment) flag: ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score -rna ``` -The same example also contains small molecule ligands which can be scored with: +The same example also contains small molecule ligands. +We can compute LDDT-PLI and BiSyRMSD with: ``` ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd --lddt-pli ``` +Example output: [compare-ligand-structures_example_out.json] + Again, it is advised to use the `-rna` flag if applicable. In this example, reference ligands are directly extracted from the provided mmCIF file based on "non-polymer" entity types.