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Superposition Panel |
The Superposition panel can be used to 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, ASL, or a SMARTS pattern.
To open the Superposition panel, you can:
Choose Tools → Superposition in the main window.
This panel is dockable, so it opens by default in the Workspace. You can change this behavior in the Preferences panel, under General – Panels.
To superimpose structures using the Superposition panel, you must first include the structures you want to superimpose in the Workspace, then define the atoms that are to be used in the superposition.
If you want to superimpose two structures, you can pick the pairs of corresponding atoms in each structure by hand. To do this, select Pick atom pairs in the Atom Pairs tab and pick one atom from each structure. The first atom in any pair must always come from the same structure, and the second from the other structure of the two. If Show markers is selected, the atom pair is connected by a dotted line, and the selected atom pair has a thicker dotted line. You can delete atom pairs by clicking Delete, or start again by clicking Delete All. After picking one pair, the Superimpose Atom Pairs button becomes active. When you click this button, the superposition is performed on the specified atom pairs, by moving the second structure over the first.
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.
If you want to superimpose many structures, or if you don't want to pick atom pairs by hand, you can define the atoms to superimpose by an ASL expression or by a SMARTS expression.
In the ASL tab, you can superimpose all atoms by clicking All, create an ASL expression from the Workspace selection by clicking Selection, enter an ASL expression in the text box, or set up the ASL expression in the Atom Selection dialog box. The superposition is performed when you click All or Selection, press ENTER in the text box, or click OK in the Atom Selection dialog box.
In the SMARTS tab, you can create a SMARTS string from the Workspace selection by clicking Get from selection, or enter a SMARTS string in the text box. The superposition is performed when you click Get from selection or press ENTER in the text box.
The structures that you superimpose need not be conformers, but if they are not, you must be careful to define atoms to superimpose that have corresponding atoms in all structures that are superimposed.
One common task is to to superimpose a number of conformers based on a subset of atoms. To do this include all the conformers in the Workspace and use the Superimpose by ASL feature or the Superimpose by SMARTS feature.
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. If you superimpose by picking atom pairs, the structure that contains the first atom picked is the reference structure. If you define the superposition atoms using ASL or SMARTS, the reference structure is the entry that has the lowest row number in the Project Table. If you want to select a particular entry as the reference structure, you can reorder the Project Table entries.
You can undo the superposition by clicking the Undo button on the Edit toolbar. The structures return to their original locations, but the RMSD values are retained in the RMSD text box. However, any property created by the superposition is removed.
You can clear the RMSD text box by clicking the Clear button.
If you want to superimpose the centers of mass of several entries, you can select them in the Workspace, then right-click and choose Align Centers of Mass.
These options specify the source of structures for the superposition. Included entries superimposes the entries in the Workspace. Selected entries superimposes the entries that are selected in the Project Table. The reference structure is the structure with the lowest row number in the Project Table.
By default, Maestro moves the structures to superimpose them. If this option is selected, the superposition is done without moving the structures. Instead, the RMS and maximum distance is calculated for the current set of atoms in their existing positions.
If you want to preserve the structures' location but perform the superposition, you can undo the transformation of the structures by clicking the Undo button on the Edit toolbar. However, if you created a property, the property creation is also undone.
If this option is selected, the RMS difference between superposition atoms is added to the entry as a property. The property is labeled "RMSD entry-ID" or "RMS In Place entry-name", where entry-ID is the reference entry (the entry on which all others are superimposed).
The Atom Pairs tab provides tools for manual selection of atom pairs for superposition.
The Superimpose by atom pairs text area displays the list of atom pairs that is used to superimpose the entries. The current pair is highlighted. You can only select one atom pair at a time.
The Delete button removes the selected atom pair from the list. The Delete All button clears the atom pair list.
Pick atom pairs option: When this option is selected, you can pick atom pairs for superposition by clicking on a pair of atoms in the Workspace. For each pair, the first atom must come from the same structure in a pair of structures, and the second from the other structure. The structures must belong to different entries.
Show Markers option: When this option is selected, Maestro connects defined atom pairs with dashed orange lines. The currently selected atom pair is distinguished by a thicker line.
Superimpose Atom Pairs button: Click this button to perform the superposition.
The ASL tab provides tools to select atoms in a structure for superimposition, using an ASL expression.
The All button selects all atoms in the
Workspace.
The Selection button uses the Workspace selection
to define the ASL expression.
The Select button opens the
Atom Selection dialog
box for setting up the ASL expression.
The text box can be used to enter the ASL expression directly. It also displays
the ASL expression generated by the three buttons.
The ASL expression (from the text box or the dialog box) is applied to each entry in turn. Then an attempt is made to superimpose corresponding atoms in turn, from the Nth entry to the 1st entry. This method is usually only useful when the structures involved are conformers.
When you click All, the superposition is done with
the maximum use of local symmetry. You can also type all in the
text box, or make a selection in the Atom Selection dialog box, but the
superposition does not use symmetry in this case, and you may get different
results as a consequence.
The SMARTS tab allows you to specify a SMARTS expression to be used for the superposition.
The Get from selection button creates a SMARTS expression from the Workspace selection. The text box can be used to enter the SMARTS expression directly. It also displays the SMARTS expression generated by the Get from selection button. You can set preferences for inclusion of notational elements in the generated SMARTS pattern in the Preferences panel, under SMARTS generation.
The SMARTS expression (from the text box or the dialog box) is applied to each entry in turn. Then an attempt is made to superimpose corresponding atoms in turn, from the Nth entry to the 1st entry. This method is usually only useful when the structures involved are conformers.
This tab allows you to superimpose protein structures using the C-alpha carbons as the atoms to superimpose. You can choose one of the entries as the fixed entry, and superimpose all the others onto this entry. To choose the entry, click Choose, and choose an entry in the dialog box that opens. The fixed entry must be one of the entries you chose for superposition. When you have chosen the fixed entry, click Superimpose to superimpose the entries.
The superposition is done starting from the first C-alpha in each protein. 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.
After two structures have been superimposed, the RMS difference between all the superposition atoms is displayed in the RMSD read-only text area. Also displayed is the maximum distance between the atoms of the most different atom pair. You can clear the text box with the Clear button.
Clear the text in the RMSD text box. The text accumulates with each RMSD calculated.
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