Grapheme TK 1.3.1

New features

  • The algorithm that determines the position of residues around a ligand has been improved. Residues are no longer placed the same distance from the ligand but are positioned closer to the ligand atoms they interact with and farther away if they have only contact interactions with the ligand.

    Example of the placement of residues around a ligand
    2016.Jun 2016.Oct
    ../../_images/ResiduePositioning_2016_Jun_pdb1c1b.png ../../_images/ResiduePositioning_2016_Oct_pdb1c1b.png
  • Clash interactions perceived by the OEPerceiveInteractionHints function are now visualized when rendering protein-ligand interactions.

    ../../_images/pdb13gs.png

    Example of visualizing Clash interactions

  • The color scheme used to visualize interaction types when depicting protein-ligand interactions has been updated.

    • The acceptor | donor color style no longer exists since OEPerceiveInteractionHints now perceives possible hydrogen bonding interactions between ligand and water. If no such interaction exists, the glyph representing a specific water residue will be left uncolored, indicating an only contact interaction.
    • Clash interactions are now colored dark red.
    Color schemes
    2016.Jun color scheme 2016.Oct color scheme
    ../../_images/DrawActiveSiteLegend_2016_Jun1.png ../../_images/DrawActiveSiteLegend_2016_Oct.png

Minor bug fixes

  • A problem that caused the glyph that represents a residue in a receptor-ligand interaction plot to be incorrectly colored based on its interaction type has been fixed.

Documentation changes

  • All images in the Grapheme TK documentation have been regenerated to reflect the changes made since the previous release.