From e95d75670e2f0cf842c1b8ef5a744b4fa2903228 Mon Sep 17 00:00:00 2001 From: Studer Gabriel <gabriel.studer@unibas.ch> Date: Mon, 19 May 2025 07:51:22 +0000 Subject: [PATCH] Edit README.md --- examples/scoring/README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/examples/scoring/README.md b/examples/scoring/README.md index d7a0ccdd..2b9afacd 100644 --- a/examples/scoring/README.md +++ b/examples/scoring/README.md @@ -47,7 +47,9 @@ ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs 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. +[action documentation](https://openstructure.org/docs/actions/) for in-depth +description of the provided data items and description of optional flags that +compute additional scores. By default, model-reference chains are aligned using Needleman-Wunsch. Many benchmarking efforts such as CASP and CAMEO assume residue numbers @@ -78,8 +80,9 @@ This only works in case of mmCIF input AND if the respective ligand is in the PDB component dictionary which defines connectivity (matching based on compound name). Container solutions come with such a dictionary which has been created at build -time. Check the Docker/Singularity instructions linked above on how to set the -latest dictionary, i.e. "Compound Library". +time. Check the detailed +[Docker](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker)/[Singularity](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity) +instructions on how to set the latest dictionary, i.e. "Compound Library". You can override automatic extraction by providing SDF files with ligand coordinates and connectivity information. If the receptor is provided in PDB format, ligands must be provided in SDF format. -- GitLab