diff --git a/singularity/README.rst b/singularity/README.rst index 7a5036b9b6b516c04b0cac5971ff7c46307b5ebc..1407509dca0972155b2bf1990d3608786539558f 100644 --- a/singularity/README.rst +++ b/singularity/README.rst @@ -65,6 +65,47 @@ Then (in the same terminal window) to invoke IPython app one can just type: To make the alias permanent put it into your ``.bashrc`` file or whatever file you use to store the aliases. +Actions +------- + +To see the list of available actions do: + + .. code-block:: + + singularity run --app OST ost.img -h + +To run chosen action do: + + .. code-block:: + + singularity run --app OST ost.img <ACTION NAME> + + +Here is an example run of the compare-structures action: + +.. code-block:: + + singularity run --app OST ost.img compare-structures \ + --model model.pdb \ + --reference reference.cif \ + --output scores.json \ + --lddt \ + --local-lddt + +In order to see all available options for this action run: + +.. code-block:: + + singularity run --app OST ost.img compare-structures -h + +CASP15 used lDDT for RNA scoring. lDDT runs stereochemistry checks by default, +removing sidechains if they have problematic stereochemistry. This gives lower +lDDT scores. The full residue is removed if the backbone has problematic +stereochemistry resulting in an lDDT score of 0.0 for that particular residue. +Stereochemistry checks for RNA were not yet available in CASP15. To reproduce +these results, use the ``--lddt-no-stereochecks`` flag. This disables +stereochemistry checks for lDDT computation but stereochemical irregularities +are still reported in the output. The Compound Library --------------------