Plot Coordinate Scan Results Panel

Plot the energies of the structures produced by a scan of one or two coordinates over a range of coordinate values.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Structure Analysis → Plot Coordinate Scan
  • Click the Tasks button and browse to MacroModel → Plot Coordinate Scan
  • Click the Tasks button and browse to Materials → Tools → More Tools → Plot Coordinate Scan
  • Click the Plot Energy by Angle button in the Rapid Torsion Scan Panel
  • Use the Workflow Action Menu for the entry group of a Jaguar scan job
  • Using
  • Features
  • Additional Resources

Using the Plot Coordinate Scan Results Panel

After a coordinate scan calculation has run, the resulting .grd file can be displayed graphically using this panel. To open a .grd file, click Load Results, and navigate to and select the file. The data from the .grd file is displayed in the plot area. Coordinate scans from the Rapid Torsion Scan Panel, from Jaguar and from MacroModel can be displayed in this panel. Only one scan can be displayed at a time. If you want to display multiple data sets on a single plot, you can use the Manage Charts Panel. If you opened a file with a two-coordinate scan, a contour plot is displayed.

If the plot shows any gaps, this means that there are data values missing in the .grd file (represented by "skip"), which in turn indicates that one of the jobs to generate data points has failed. You should check the output for the scan jobs to see which job failed.

Plot Coordinate Scan Results Panel Features

Load Results button

Load the results of a scan for plotting. Opens a file selector, in which you can locate and load a grid file (.grd) for the scan.

Edit text button


Edit the text of the plot title and axis labels. Opens the Edit Text Labels dialog box. Editing the y-axis label is disabled for one-coordinate scans.

Save Plot option menu

Save the plot as an image, or export the plot data to a CSV file. Each item opens a file selector that you can use to save the file in an appropriate format.

Plot area

This area displays the plot of the energies as a function of the coordinate for a one-coordinate scan, and a contour plot of the energies for a two-coordinate scan. If opened from the Rapid Torsion Scan Panel, the original angle is marked with a vertical green line. The energetically accessible range (5 kcal/mol) can also be displayed.

If you click a plot point, the corresponding structure is displayed in the Workspace.

Breaks in the plot indicate missing data for plot points. This happens if the job to generate the data for the point fails.

Energy Options option menu

Select options for the units and the energy scale, and turn on or off the display of the energetically accessible range (5 kcal/mol) from the lowest energy point. The energetically accessible range feature is not present for two-coordinate scans.

Axis Ranges button

Set the axis ranges, i.e. the minimum and maximum values to plot on the x and y axes. Opens a dialog box in which you can set the ranges.

This button is only available for a one-coordinate scan.

Contours button

Set up the contours for the plot. Opens the Specify Contours Dialog Box.

This button is only available for a two-coordinate scan.

Reset button

Clear all data in the panel and reset the settings to the defaults.

Tutorials

Related Topics