From 56c80161cc2d0ce16e69840c49c71b47745f604c Mon Sep 17 00:00:00 2001 From: Studer Gabriel <gabriel.studer@unibas.ch> Date: Tue, 18 Feb 2025 10:26:58 +0000 Subject: [PATCH] Edit README.md --- examples/scoring/README.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/examples/scoring/README.md b/examples/scoring/README.md index 2345c4bbc..8125cb602 100644 --- a/examples/scoring/README.md +++ b/examples/scoring/README.md @@ -9,7 +9,7 @@ OpenStructure provides "actions" for general benchmarking use cases. polymer entities and non-polymer entities, i.e. small molecule ligands The example commands here assume an OpenStructure installation -(compile instructions: https://openstructure.org/docs/dev/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 @@ -34,7 +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) +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. By default, model-reference chains are aligned using Needleman-Wunsch. Many benchmarking efforts such as CASP and CAMEO assume residue numbers @@ -54,6 +56,8 @@ ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd ``` 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. 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 -- GitLab