Superposition Panel
Perform rigid-body superposition of the structures that are included in the Workspace, or the structures that are selected in the Project Table, based on corresponding atom pairs defined by selection, maximum common substructure, predefined atom sets, ASL, or a SMARTS pattern.
To open this panel: click the Tasks button and browse to Structure Alignment → Superposition.
- Using
- Features
- Additional Resources
Using the Superposition Panel
When you superimpose structures, the structures are moved to minimize the RMS distance between the selected atoms in each structure and the corresponding atoms in the reference structure. This means that the substructure or set of atoms you choose for performing the RMSD calculation must exist in all structures. For example, if you choose to superimpose on the ligand, it must be the same ligand in each entry, otherwise it is not possible to determine the corresponding atoms. For the Maximum Common Substructure method, there must be a common substructure between each superimposed entry and the reference, which need not be the same for all of the entries. For superposition of backbones or C-alpha atoms, the superposition is done starting from the first residue. This feature is mainly useful for very similar proteins - for example, mutants of a parent protein. If you want to take sequence alignment into account, you should instead use the Protein Structure Alignment Panel. There are various other ways of aligning structures that have other features—see Aligning Structures for more information.
Superposition can be undone (in the Maestro main window, choose Edit → Undo).
Superposition Panel Features
- Entries to superimpose options
- Reference structure option menu
- RMSD options
- Choose Method options and controls
- Superimpose Structures button
- Compute RMSD button
- Results table
- Entries to superimpose options
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Choose the source of entries to superimpose:
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Workspace—superimpose the entries that are included in the Workspace. If you choose Atom pairs for the method, there must be only two entries in the Workspace.
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Project Table (selected)—superimpose the entries that are selected in the Project Table (or Entry List). If you select this source, the Atom pairs method is disabled, as it requires picking in the Workspace.
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- Reference structure option menu
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Choose the reference structure from among the entries to superimpose. The default is the entry with the lowest row number in the Project Table. The menu is updated as you change the included or selected entries.
- RMSD options
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Choose options for calculating the RMSD and using it to superimpose structures.
- Compute without changing structures option
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By default, Maestro moves the structures to superimpose them, changing the coordinates. If this option is selected, the RMS and maximum distance are calculated for the current set of atoms in their existing positions, and the structures are not moved.
- Add property to Project Table option
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If this option is selected, the RMS difference between superposition atoms is added to each entry as a property. The property is labeled "RMSD entry-ID" if the structures were superimposed, and represents the RMSD after superposition, or "RMS In Place entry-name" if the structures were not superimposed, where entry-ID is the reference entry (the entry on which all others are superimposed).
- Choose Method options and controls
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Choose the method for determining the atoms to be superimposed. The choice of option affects the tools that are displayed below.
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Substructures—superimpose atoms in a substructure, which can be defined in multiple ways. The Define substructures for superposition using option menu is displayed, which allows you to choose the substructure. Tools for defining the substructure are displayed depending on the choice from this option menu.
You must be careful to define substructures to superimpose that have corresponding atoms in all structures that are superimposed.
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Atom pairs—superimpose the two structures by picking corresponding atom pairs. Tools for atom pairs are displayed below. This option is not available if Project Table (selected) is chosen as the source of entries to superimpose.
The superposition depends on how many atom pairs you pick. If you pick one pair, a simple translation is performed. If you pick two pairs, the vector between the two atoms in the second structure is aligned to the vector between the two atoms in the first, and the centroids of the vectors are made to coincide. For three atom pairs, the structure is rotated and translated so that the three atoms coincide. For more atom pairs, the RMSD of the atom pairs between the structure is minimized to determine the best superposition.
- Define substructures for superposition using option menu
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Choose the type of substructure to superimpose. In addition to a range of predefined substructures, such as backbones, membrane, ligand, you can choose to specify the substructure by ASL or SMARTS, or use the maximum common substructure (the default). If you choose Maximum Common Substructure, the structures to superimpose must not have more than 255 atoms. The predefined substructures should be closely related: conformers, or structures where the ASL definition matches a consistently numbered set of atoms in each structure.
Choosing ASL or SMARTS displays standard tools for specifying a query of the chosen type. Choosing Custom Set opens the Superposition - Choose Custom Set dialog box, which lists the available sets. Select a set from the list and click OK to use this set.
- ASL tools
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Enter the ASL query in the text box to define the substructure, or use the buttons to add standard objects, the Workspace selection, or a custom ASL query to the query. See Picking Tools for a description of the tools.
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- SMARTS text box and
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Enter the SMARTS pattern for the substructure in the text box, or select the atoms in the Workspace for the SMARTS pattern and click
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- Atom pairs tools
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When you select Atom pairs as the method, the following tools are displayed.
- Define atom pairs to overlay list
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This list shows the atom numbers of the atom pairs that you pick in the Workspace. You can select a single row in the list, for deletion. The currently selected atom pair is distinguished in the Workspace by a thicker line.
- Pick button
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When selected (highlighted), you can pick the atom pairs in the Workspace. A box is displayed around the first atom you pick. When you pick the second atom, the atom pair is connected with dashed orange lines. You must pick one atom from each entry, but the order in which you pick the atoms does not matter.
- Delete and Delete All buttons
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Click Delete to delete the selected list item; click Delete All to clear the list.
The superposition depends on how many atom pairs you pick. If you pick one pair, a simple translation is performed. If you pick two pairs, the vector between the two atoms in the second structure is aligned to the vector between the two atoms in the first, and the centroids of the vectors are made to coincide. For three atom pairs, the structure is rotated and translated so that the three atoms coincide. For more atom pairs, the RMSD of the atom pairs between the structure is minimized to determine the best superposition.
Perform the superposition and report the RMSD, or just report the RMSD without performing the superposition. The button changes text when you select or deselect Compute without changing structures.
Show the results of the superposition. Each row represents an entry pair, one of which is the reference entry (and is marked with a *). The method and the RMSD are reported along with the titles of the entry pair.
The table has a menu button at the right which allows you to view details for a single pair or copy the details to the clipboard, select all rows, and export the selected rows to a CSV file.
The table shortcut menu allows you to view the details for a single row, copy the contents of the selected rows to the clipboard, copy the contents of the cell you clicked in to the clipboard, and export the selected rows to a CSV file.