Calculate Average Structure Panel

Calculate the weighted average structure from a set of conformers selected in the Project Table. Either the average structure (which might not have physical geometry) is added to the Project Table, or the input structure closest to the average structure (the "representative" structure) is selected and placed in the Workspace. The RMSD from the average structure can be added as a property to each structure.

To open this panel: click the Tasks button and browse to Structure Analysis → Average Structure.

  • Features

Calculate Average Structure Panel Features

Average calculation mode options

Select the option for the result you want from the calculation. The weighted average structure is always calculated.

  • Generate average structure—Add the weighted average structure to the Project Table. This structure is likely to be unphysical, as it involves averaging the coordinates of each atom.
  • Select representative structure—Select the structure with the smallest RMSD from the average structure and place it in the Workspace.
Weighting method options

Select an option for weighting the structures in the average structure.

  • Uniform weighting—Use the same weight for each structure.
  • Property weighting—Weight the structures by the value of a property. Clicking Choose Property opens a property selector, in which you can choose the property from those available in the project. Filtering by family and by text matching is available in the property selector. The property is displayed in the text box next to the button.
  • Boltzmann weighting—Weight the structures by their Boltzmann population at a specified temperature. You can set the temperature in the Temperature text box. The populations are calculated from a specified energy property, which you choose by clicking Choose Property and making a choice from the project properties in the property selector that opens. Filtering by family and by text matching is available in the property selector. The energy units can be set by choosing one of the Property scale options.
Before calculation, superimpose all on first selected entry option

Superimpose the selected entries on the first selected entry before calculating the average structure. This action changes the coordinates of all of the selected structures except the first (which is used as the reference).

Atoms for RMSD options

Select an option for superimposing the structures and calculating the RMSD for the structures, from All atoms, Heavy atoms and polar hydrogens (all atoms except nonpolar hydrogens), and Heavy atoms (no hydrogens). The RMSD calculation is used for selecting the representative structure.

Check symmetry in RMSD comparisons

When comparing structures for the RMSD, check for local symmetry in the connectivity (such as ring orientation) that could reduce the RMSD, and use the lowest RMSD value.

Create RMSD-to-Avg property in Project Table option

Create a project property that stores the RMSD between the structures and the average structure, named RMSD-to-Avg.

Close after running option

Close the panel after the job has been run.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes 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.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.