diff --git a/doc/source/tutorials/alchemical_transfer.rst b/doc/source/tutorials/alchemical_transfer.rst index 0ce5afc6..f354a592 100644 --- a/doc/source/tutorials/alchemical_transfer.rst +++ b/doc/source/tutorials/alchemical_transfer.rst @@ -88,8 +88,9 @@ more choices to be made before the system can be prepared. The most important of these is the choice of displacement vector, which defines the direction and distance at which the free ligand will be placed relative to the bound ligand. It is generally recommended that this displacement be at least 3 layers of water -molecules (> 10 Å) thick. If no displacement is provided a default choice of -[20Å, 20Å, 20Å] will be used. +molecules (> 10 Å) thick. If no displacement is provided BioSimSpace will find a +best guess translation vector based on the relative positions of the protein and +bound ligands and translate the free ligand 20 Å along this vector. This is also the point at which a custom set of atoms can be chosen to define the centre of mass of both the ligands and the protein. In the majority of cases it diff --git a/doc/source/tutorials/images/tyk2_prepared.png b/doc/source/tutorials/images/tyk2_prepared.png index df34cfce..0725e5d2 100644 Binary files a/doc/source/tutorials/images/tyk2_prepared.png and b/doc/source/tutorials/images/tyk2_prepared.png differ