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Commit 56c80161 authored by Studer Gabriel's avatar Studer Gabriel
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Edit README.md

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......@@ -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
......
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