Nanoreactor Viewer Panel

Plot the results of a nanoreactor calculation. When a calculation run from the Nanoreactor Panel is complete, the lowest energy structures are returned as a group in the Project Table. These structures can be loaded into this panel to visualize the relative energies of the products. Hover on any data point to see the 2D structure and click on the data point to include the structure in the workspace.

To display this panel: click the Tasks button and browse to Materials → Quantum Mechanics → Reaction Network → Nanoreactor Results

To open this panel from the entry group for the results of a job, and load the results, use the Workflow Action Menu .

The following licenses are required to use this panel: MS Maestro, MS Reactivity

  • Features
  • Additional Resources

Nanoreactor Viewer Panel Features

Load Selected Entries button

Load the selected structures from a calculation run using the Nanoreactor Panel. The number of entries loaded is indicated by the text to the right of the button.

xTB Energy tab

Plots the xTB optimized reactants and products as a function of relative xTB free energy. The structures shown on the x-axis depend on the Plot structures within N kcal/mol of the lowest energy structure text box.

Plot structures within N kcal/mol of the lowest energy structure text box

Specify the maximum relative energy value of interest in kcal/mol. The specified energy is relative to the lowest energy structure. All structures with relative energies smaller than or equal to the specified value are plotted.

Plot buttons

Use these buttons to configure the plot.

  • Zoom In—Zoom in on the plot. Each click zooms in by a predefined factor, enlarging the view of the current center of the plot. You can also zoom in on a particular area by dragging out a rectangle.
  • Zoom Out—Zoom out by a predefined factor. Each click zooms out by a predefined factor, to show more of the plot.
  • Axes—Set the range and labeling options for the axes. Opens the Axes Parameters Dialog Box.
  • Reset View—Reset the view of the plot to the original zoom and pan values.
  • Series—Set up the appearance of the plot series, such as color, symbol, lines. Opens the Series Parameters Dialog Box.
  • Copy—copy an image of the plot to the clipboard, for use in other applications.
Legend option

Display a legend in the plot.

Plot area

This area displays the relative xTB free energy in kcal/mol for a specified set of structures. The number of structures shown is determined by the energy threshold specified in the Plot structures within N kcal/mol of the lowest energy structure text box. Pause the pointer over any data point to see the energy and a 2D preview of the structure. Click on the data point to include the structure in the workspace.

Refined Energy tab

Plots the xTB optimized reactants and products as a function of relative refined free energy. The structures shown on the x-axis depend on the Plot structures within N kcal/mol of the lowest energy structure of the lowest energy structure text box. This plot is only available if the Refine final energy option is selected in the Nanoreactor Panel when running the calculation.

Plot structures within N kcal/mol of the lowest energy structure text box

Specify the maximum relative energy value of interest in kcal/mol. The specified energy is relative to the lowest energy structure. All structures with relative energies smaller than or equal to the specified value are plotted.

Plot buttons

Use these buttons to configure the plot.

  • Zoom In—Zoom in on the plot. Each click zooms in by a predefined factor, enlarging the view of the current center of the plot. You can also zoom in on a particular area by dragging out a rectangle.
  • Zoom Out—Zoom out by a predefined factor. Each click zooms out by a predefined factor, to show more of the plot.
  • Axes—Set the range and labeling options for the axes. Opens the Axes Parameters Dialog Box.
  • Reset View—Reset the view of the plot to the original zoom and pan values.
  • Series—Set up the appearance of the plot series, such as color, symbol, lines. Opens the Series Parameters Dialog Box.
  • Copy—copy an image of the plot to the clipboard, for use in other applications.
Legend option

Display a legend in the plot.

Plot area

This area displays the relative refined free energy in kcal/mol for a specified set of structures. The number of structures shown is determined by the energy threshold specified in the Plot structures within N kcal/mol of the lowest energy structure text box. Pause the pointer over any data point to see the energy and a 2D preview of the structure. Click on the data point to include the structure in the workspace.

xTB vs Refined Free Energy tab

Plots the relative xTB free energy as a function of the relative refined free energy for the xTB optimized reactants and products. This plot is only available if the Refine final energy option is selected in the Nanoreactor Panel when running the calculation.

Plot buttons

Use these buttons to configure the plot.

  • Zoom In—Zoom in on the plot. Each click zooms in by a predefined factor, enlarging the view of the current center of the plot. You can also zoom in on a particular area by dragging out a rectangle.
  • Zoom Out—Zoom out by a predefined factor. Each click zooms out by a predefined factor, to show more of the plot.
  • Axes—Set the range and labeling options for the axes. Opens the Axes Parameters Dialog Box.
  • Reset View—Reset the view of the plot to the original zoom and pan values.
  • Series—Set up the appearance of the plot series, such as color, symbol, lines. Opens the Series Parameters Dialog Box.
  • Copy—copy an image of the plot to the clipboard, for use in other applications.
Legend option

Display a legend in the plot.

Plot area

This area displays the relative xTB free energy of all structures resulting from the nanoreactor calculation as a function of relative refined free energy in kcal/mol. Pause the pointer over any data point to see the energies and a 2D preview of the structure. Click on the data point to include the structure in the workspace.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Tutorials

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