Document action usage in singularity container

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
 --------------------