diff --git a/examples/scoring/README.md b/examples/scoring/README.md index bb277ae73e01dc83279374285eef32c91ca332cc..b4efd15908441d980de991eb6147359050f747d4 100644 --- a/examples/scoring/README.md +++ b/examples/scoring/README.md @@ -34,9 +34,9 @@ default output (out.json): ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score ``` -An example output can be found [here](compare-structures_example_out.json) and -we refer to the action documentation for in-depth description of the provided -data items. +Results should be computed within seconds and example output can be found +[here](compare-structures_example_out.json). We refer to the action +documentation for in-depth description of the provided data items. By default, model-reference chains are aligned using Needleman-Wunsch. Many benchmarking efforts such as CASP and CAMEO assume residue numbers @@ -55,9 +55,9 @@ We can compute LDDT-PLI and BiSyRMSD with: ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd --lddt-pli ``` -An example output can be found [here](compare-ligand-structures_example_out.json) -and we refer to the action documentation for in-depth description of the provided -data items. +Results should be computed within seconds and example output can be found +[here](compare-ligand-structures_example_out.json). We refer to the action +documentation for in-depth description of the provided data items. 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