From 4428dc43c236e0372841731168c41209d0682f04 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 10 Mar 2023 09:56:37 +0100
Subject: [PATCH] doc: SCHWED-5481 document structure format
---
actions/ost-compare-ligand-structures | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index a9eb8c72b..f9199342b 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -7,8 +7,9 @@ Example: ost compare-ligand-structures \\
-r reference.cif \\
--lddt-pli --rmsd
-Only minimal cleanup steps are performed (remove hydrogens, and for structures
-only, remove unknown atoms and cleanup element column).
+Structures of polymer entities (proteins and nucleotides) can be given in PDB
+or mmCIF format. If the structure is given in mmCIF format, only the asymmetric
+unit (AU) is used for scoring.
Ligands can be given as path to SDF files containing the ligand for both model
(--model-ligands/-ml) and reference (--reference-ligands/-rl). If omitted,
@@ -19,6 +20,12 @@ For structures given in PDB format, this is based on the HET records and is
normally not what you want. You should always give ligands as SDF for
structures in PDB format.
+Polymer/oligomeric ligands (saccharides, peptides, nucleotides) are not
+supported.
+
+Only minimal cleanup steps are performed (remove hydrogens, and for structures
+of polymers only, remove unknown atoms and cleanup element column).
+
Ligands in mmCIF and PDB files must comply with the PDB component dictionary
definition, and have properly named residues and atoms, in order for
ligand connectivity to be loaded correctly. Ligands loaded from SDF files
--
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