Ligand Designer - Display Settings Dialog Box
Make display settings for objects in the Workspace placed by the Ligand Designer.
To open this dialog box, click the Settings link in the Display section of the Ligand Designer Panel.
- Features
- Additional Resources
Ligand Designer - Display Settings Dialog Box Features
- Growth Space tab
- Potential Interactions tab
- Displaceable Waters tab
- Replaceable Waters tab
- Surfaces tab
- Reset button
- Growth Space tab
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Make settings for the display of the growth space regions in the Workspace.
- Colors section
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Make settings for the colors used and objects displayed. The current colors are shown on the buttons. Clicking the button opens a color selector.
- Default option
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Display the growth space for the default of a single receptor. This option is selected by default if a single receptor was analyzed. If you select this option with two receptors analyzed, Receptor 2 (secondary) is removed from the Workspace.
- Two receptors option
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Display the growth space for two receptors, with coloring to distinguish the space that originates from each or both receptors. This option is selected by default if two receptors were analyzed. You can switch to the single receptor case (Default option) and back; the secondary receptor is removed from the Workspace when you switch and restored to the Workspace when you switch back.
- Unique to Receptor 1 option and color button
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Display the growth space arising from receptor 1 but not receptor 2 in the color selected with the color button. The entry title for receptor 1 is shown to the right of the color button.
- Unique to Receptor 2 option and color button
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Display the growth space arising from receptor 2 but not receptor 1 in the color selected with the color button. The entry title for receptor 2 is shown to the right of the color button.
- Common option and color button
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Display the growth space arising from both receptor 1 and receptor 2 in the color selected with the color button.
- Residue backbone clashes option
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Display clashes of the ligand with the backbone residues. This option is on by default for a single receptor, off by default for two receptors.
- Residue backbone clash (bad) color button
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Set the color for clashes between residue backbone atoms and the ligand that are classified in Maestro as bad. See Pi-Pi and Contact Criteria settings for information on the classification.
- Residue backbone clash (ugly) color button
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Set the color for clashes between residue backbone atoms and the ligand that are classified in Maestro as ugly. See Pi-Pi and Contact Criteria settings for information on the classification.
- Show legend option
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Show a legend in the Workspace that describes the coloring of the growth space regions.
- Potential Interactions tab
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Set colors and quantity of the markers that show interactions with the protein.
- Colors section
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Set colors for the different types of interactions. The color buttons show the current color; clicking the button opens a color selector.
- Interactions section
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Specify the quantity of interaction markers ("features") that you want to see in the Workspace. The slider has three settings.
- Displaceable Waters tab
- Replaceable Waters tab
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These tabs allow you to set options for displaying waters that are displaceable or replaceable. Displaceable waters are ones that are unstable, usually near a hydrophobic region; replaceable waters are stable and could be replaced by a group that has similar interactions (e.g. acceptor or donor).
The settings in these tabs allow you to define what a displaceable or replaceable water is in terms of thermodynamics, and restrict the water locations to display. These tabs are only active if you have one or more water maps in the Workspace. See Water sites table for detailed information on the four quantities that you can use to select waters. The waters from different water maps are shown with different shapes (as for the WaterMap - Examine Results Panel).
- Enthalpy (ΔH) option, text boxes and slider
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Show only waters whose enthalpy lies within the range specified by the values in the text boxes. Use either the slider or the text boxes to adjust the values.
- Entropy (-TΔS) option, text boxes, and slider
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Show only waters whose entropy lies within the range specified by the values in the text boxes.
- Free Energy (ΔG) option, text boxes, and slider
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Show only waters whose free energy lies within the range specified by the values in the text boxes.
- Overlap Factor option, text boxes, and slider
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Show only waters whose fractional overlap with the ligand lies within the range specified by the values in the text boxes.
- Distance from active ligand option and text box
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Show only waters within the specified distance from the active ligand. The maximum distance for which waters are shown is 6 Å.
- Show only waters in growth space option
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Show only waters that are inside the growth space, both in cavity spaces and in solvent-exposed spaces. If this option is unchecked, all waters in the Water Map are shown.
- Color sites by option menu
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Choose a scheme for coloring the water sites by various schemes, including the thermodynamic properties of the site. The schemes are as follows:
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ΔG (simple)—green for more negative values, red for more positive values.
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ΔG (red -blue)—blue for more negative values, red for more positive values.
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ΔH and -TΔS—Brighter cyan for lower enthalpy, brighter yellow for lower entropy. Both are applied, so brighter green has lower enthalpy and entropy.
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Entry—Color all sites from the same entry with the same color, using the Maestro Color by Entry color scheme. If both replaceable and displaceable waters are displayed, they are distinguished by using different shades of the colors.
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- Surfaces tab
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Make settings for the display of surfaces. For more information on the color schemes, see Coloring Atoms.
- Protein section
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Make settings for the receptor surface.
- Color scheme option menu
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Select a color scheme for the surface. For structure-based schemes, the color applied to the surface is that of the nearest atom, when the atoms are colored by the scheme.
- Display surface within N Å of the initial active ligand
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Display the parts of the surface that are within the specified distance of the initial active ligand, i.e. the ligand that was included in the Workspace for the initial analysis. The maximum distance for which the surface is displayed is 5 Å.
- Ligand section
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Make settings for the ligand surface.
- Reset button
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Reset the dialog box to its default settings, clearing all changes.