diff --git a/examples/scoring/README.md b/examples/scoring/README.md index b8500ab9564c342d8a04ce0704e01c8e91b2f937..d7a0ccdd69ca3929885da8fa5476d3c36dccc2b1 100644 --- a/examples/scoring/README.md +++ b/examples/scoring/README.md @@ -19,10 +19,10 @@ unzip -j example.zip # Run the examples The example commands here assume an OpenStructure installation -(compile instructions: https://openstructure.org/docs/install/). +([compile instructions](https://openstructure.org/docs/install/)). Running the computations in containers provide a considerably easier setup than compiling OpenStructure from source. Instructions for setup and running -equivalent computations are available for +equivalent computations are available below for * [Docker](#docker) * [Singularity](#singularity) @@ -45,9 +45,9 @@ default output (out.json): ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score ``` -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. +Results should be computed within seconds and saved in the `out.json` file +([see example output](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 @@ -66,9 +66,10 @@ We can compute LDDT-PLI and BiSyRMSD with: ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd --lddt-pli ``` -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. +Results should be computed within seconds and saved in the `out.json` file +([See example output ](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