diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures index b4a192631f961f54e07059a56057c839f2651007..ff579be64c219ea4029389fb6be4c23eda099d13 100644 --- a/actions/ost-compare-structures +++ b/actions/ost-compare-structures @@ -13,8 +13,10 @@ eg. --remove oxt hyd \\ --map-nonstandard-residues -If desired one can recreate what CAMEO is calculating. CAMEO calls lddt binary -as follows: +Here we describe how the parameters can be set to mimick a CAMEO evaluation +(as of August 2018). + +CAMEO calls the lddt binary as follows: lddt \\ -p <PARAMETER FILE> \\ diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst index 1d22faf44e6cc8890ffd2a621c49fb0d35da0ed3..4ff4afc6aabf48fc88e8fb75ec9a717e51a19f5a 100644 --- a/modules/doc/actions.rst +++ b/modules/doc/actions.rst @@ -109,7 +109,12 @@ Example usage: $ curl https://www.cameo3d.org/static/data/modeling/2018.03.03/5X7J_B/bu_target_01.pdb > reference.pdb $ curl https://www.cameo3d.org/static/data/modeling/2018.03.03/5X7J_B/servers/server11/oligo_model-1/superposed_oligo_model-1.pdb > model.pdb - $ $OST_ROOT/bin/ost compare-structures --model model.pdb --reference reference.pdb --output output.json --qs-score --residue-number-alignment --lddt --structural-checks --consistency-checks --inclusion-radius 15.0 --bond-tolerance 15.0 --angle-tolerance 15.0 --molck --remove oxt hyd unk --clean-element-column --map-nonstandard-residues + $ $OST_ROOT/bin/ost compare-structures \ + --model model.pdb --reference reference.pdb --output output.json \ + --qs-score --residue-number-alignment --lddt --structural-checks \ + --consistency-checks --inclusion-radius 15.0 --bond-tolerance 15.0 \ + --angle-tolerance 15.0 --molck --remove oxt hyd unk \ + --clean-element-column --map-nonstandard-residues ################################################################################ Reading input files (fault_tolerant=False) @@ -345,7 +350,7 @@ In the example above the output file looks as follows: } } -If only all the structures are clean one can omit all the checking steps and +If all the structures are clean one can omit all the checking steps and calculate eg. QS-score directly: .. code:: console