Merge branch 'develop' into CASP13

actions/ost-compare-structures

@@ -307,8 +307,8 @@ def _ParseArgs():
               " * oxt - remove terminal oxygens\n"
               " * nonstd - remove all residues not one of the 20\n"
               " * standard amino acids\n"
-              " * unk - Remove unknown and atoms not following the"
-              "nomenclature"))
+              " * unk - Remove unknown and atoms not following the\n"
+              "         nomenclature"))
     parser.add_argument(
         "-ce",
         "--clean-element-column",

modules/doc/actions.rst

@@ -23,8 +23,8 @@ lDDT scores between two complexes from the command line with:
                            [-o OUTPUT] [-d] [-ds DUMP_SUFFIX]
                            [-rs REFERENCE_SELECTION] [-ms MODEL_SELECTION]
                            [-ca] [-ft] [-cl COMPOUND_LIBRARY] [-qs]
-                           [-c CHAIN_MAPPING [CHAIN_MAPPING ...]] [-rna]
-                           [-l] [-ir INCLUSION_RADIUS]
+                           [-c CHAIN_MAPPING [CHAIN_MAPPING ...]]
+                           [--qs-rmsd] [-rna] [-l] [-ir INCLUSION_RADIUS]
                            [-ss SEQUENCE_SEPARATION] [-spr] [-ml]
                            [-rm REMOVE [REMOVE ...]] [-ce] [-mn] [-sc]
                            [-p PARAMETER_FILE] [-bt BOND_TOLERANCE]