Prime Energy Visualizer Panel
Visualize the Prime energy and its components from an Analyze Energy job, a WM/MM job or an MM-GBSA job. The visualization colors the structure in the Workspace and the surface (if generated) by the values of a chosen property or sum of properties.
To open this panel, click the Tasks button and browse to Biologics → Visualize Energy.
- Using
- Features
- Additional Resources
Using the Prime Energy Visualizer Panel
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Display a structure in the Workspace for which a Prime calculation has been run.
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Choose the property family from the Family option menu.
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Select the property or properties to display.
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Click Visualize to color the structure by the values of the property selected, or the sum of the property values.
Prime Energy Visualizer Panel Features
Visualize section
This section contains the main visualization controls.
- Family option menu
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Choose the property family to display from this option menu. The properties listed under Property are updated to reflect your choice. The option menu shows all possible choices, but there might not be values for the properties for all of these choices, depending on the calculation you performed for the Workspace structure.
- Property options
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The controls under this heading depend on whether there is a structure in the Workspace and whether it has the appropriate properties.
If the property family chosen from the Family option menu is present, controls for visualization of the property components are displayed. Some have only one component, which is selected by default. For others, there are multiple components, and you can choose to show the total property value or sum of selected components. When you choose the Sum of selected property components option, the check boxes for the individual components are made available. The values for the components are weighted according to their contribution to the total property value. Selecting multiple components displays the sum of the contributions from those components.
If you select Prime energy (residue interactions) from the Family option menu, you must pick a residue in the Workspace to show the interactions for the selected energy components. The residue you pick is displayed in the Residue for interaction display text box. The Pick a residue option is selected by default, for picking the desired residue.
If the Workspace structure does not have the required property values, the controls are replaced with a warning message indicating what type of job to run to generate the data. A button is displayed to run the job immediately, for properties coming from a Prime energy calculation. For jobs that take a longer time, a button is displayed to open the required panel to run the job. For properties produced by a Prime energy calculation, all the settings from the Calculate Energy Panel can be displayed so you can run a nondefault calculation.
If the Workspace is empty, a message is displayed prompting you to include a structure in the Workspace.
Colors and Surfaces button
Clicking this button shows or hides the Colors and Surfaces tabs.
Colors tab
This tab allows you to set up the coloring for the visualization.
- Scheme option menu
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Four color schemes are available: green-white-red, blue-white-red, blue-red, and rainbow. The blue or green values represent low energies or favorable values, the red values represent high energies or unfavorable values. In addition, you can choose None to color the atoms by element. This can be useful when labeling atoms by the property values rather than coloring them.
- Label atoms option
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Select this option to label the atoms with the property values. The labels are colored by the atom color.
- Ramping option menu
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Ramping determines the mapping of numerical values for the currently selected properties to colors. The ramp is simply defined by a minimum and maximum value: anything below the minimum is colored the same as the minimum, and anything above the maximum is coloured the same as the maximum. Values in between are scaled linearly along the currently selected color ramp. Available ramp settings are:
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Fixed—Use hard-wired minimum and maximum values that were chosen to give the most broadly useful range of colors. Each property has its own Min and Max values that are set according to the usual range of property values. If multiple properties are shown, the Min and Max values are set to the smallest of the Min values for the selected properties and the largest of the Max values.
Many of the terms have different inherent ranges. For example, the ramp for Pi-Pi packing is [−0.08,0.08], whereas the ramp for Electrostatic is [−20.0,20.0]. If you visualize Pi-Pi packing by itself, the overall ramp will be [−0.08,0.08], and the various pi-pi interactions will show up as strong blue. However, visualizing Pi-Pi packing in combination with Electrostatic means the overall ramp will be [−20.0,20.0], and the pi-pi contributions will be very subtle in comparison to the electrostatic contributions.
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Adaptive—Use the maximum and minimum values over the currently selected properties as the end points for the color This choice can be useful for amplifying the differences in the current structure, to better differentiate the variations. However, if the properties only have favorable values, some of these values are colored red, which otherwise indicates that the values are unfavorable. In this context it means that they are the least favorable.
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Custom—Use the values given in the Min and Max text boxes as the ends of the ramp. These values are applied to all properties, which places them on the same scale. You can use the Auto-detect button to set the values in the Min and Max text boxes to the minimum and maximum property values found in the Workspace structure.
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- Min and Max text boxes
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Specify the property values for the two ends of the color ramp.
- Auto-detect button
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Set the values in the Min and Max text boxes to the minimum and maximum property values found in the Workspace structure.
- Color smoothing slider
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Spread the color over neigboring atoms, by performing some averaging over the property values. This slider is absent if there is only one property in the family.
- Merge values for option menu
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Merge the property values for the selected structural features. The values are summed for the atoms in the feature, and each atom is assigned the summed value. You can merge values for hydrogens into the attached heavy atoms, or merge values for entire residues. This menu is absent if there is only one property in the family.
Surfaces tab
This tab provides controls for creating and displaying a molecular surface, which is colored by the color of the nearest atom. The color is updated as you change the property that is used to color the atoms, so it is only necessary to create one surface.
- Resolution option menu
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Specify the resolution of the grid used to create the surface, and hence the quality of the surface. See the Advanced Surfaces Panel topic for details.
- Style options
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Choose the style for the surface, from Solid, Mesh, and Dot. Only Solid is affected by the value of Transparency. Mesh and Dot are always drawn fully opaque.
- Transparency controls
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These controls affect how transparent or opaque the surface is. Transparency only affects surfaces drawn in Solid style. Other styles are always drawn fully opaque.
- Sliders and text boxes
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Drag the slider to change the transparency of the front or back of the surface, or enter the transparency in the text box.
- Adjust together option
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Select this option (the default) to apply the same transparency to both front and back of the surface. When selected, dragging one slider or entering a value in one of the text boxes changes the value for the other side of the surface. Deselect this option to adjust the transparency of the front and back of the surface independently.
- Hide Surface option
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Show or hide the surface. This allows you to switch between display of properties on the surface and display of properties on the structure.
- Create Surface button
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Create a molecular surface, and color it by the color of the nearest atom. The color is updated as you change the property that is used to color the atoms, so it is only necessary to create one surface.
Visualization controls
These controls are used perform the visualization, manually or automatically.
Residue interactions are automatically visualized, so these controls are unavailable if you select Prime energy (residue interactions).