From 52cdce934a3b6de173d74fe1bc6d18f6f24e9d2e Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 14 Aug 2018 15:00:53 +0200
Subject: [PATCH] Doc update
---
actions/ost-compare-structures | 6 ++++--
modules/doc/actions.rst | 9 +++++++--
2 files changed, 11 insertions(+), 4 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index b4a192631..ff579be64 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 1d22faf44..4ff4afc6a 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
--
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