If you want to determine the similarity of structures such as a set of conformers or a family of ligands docked by Glide, you can display the structures in the Workspace and then use the tools in theSuperpositionpanel to superimpose the structures and evaluate the differences in the atom positions. Each structure must be in a separate project entry.
To open theSuperposition panel, chooseSuperposition from theTools menu.
The superposition scheme works by aligning the first selected atom in each structure, then attempting to align the second selected atom, and so on. The atoms are aligned to the first entry in the Project Table that is being used in the superposition (the reference entry). After superim- posing atoms, the results of the operation are displayed in theRMSDtext box near the bottom of the panel. The results include the molecule numbers, the RMS deviation of the atoms from those of the first structure, and the maximum difference between superimposed atom positions. There are two choices for the entries that are used for the superposition: the included entries (those in the Workspace), or the selected entries (those selected in the Project table). This choice is available underEntries to superimpose.If you choose Selected entries, you must have at least one entry displayed in the Workspace to be able to pick atoms for superposition. There are three choices for the method of superposition:
• Superimpose by atom pairs—To compare two structures, you can select the atoms to superimpose in each structure in pairs. To define the atom pairs, selectPick atom pairs, then pick the atom pairs. You must pick one atom from each entry, and you must pick the first atom from the same entry each time. The atom pairs are displayed in theSuperim- pose by atom pairstext box as you pick them. IfShow markersis selected, the atom pairs are connected by dashed lines. Once you have picked the first pair,Superimpose Atom Pairs,Delete, andDelete Allare activated. If you need to delete a pair, select the pair in the list and clickDelete. To delete all pairs, clickDelete All. After all the atom pairs are
Figure 9.4. The Superposition panel.
If you want to compare more than two structures or if picking individual pairs is not prac- tical, you can superimpose atoms defined by an ASL expression or by a SMARTS pattern.
• Superimpose by ASL—To superimpose the displayed or selected structures based on all the atoms in the structures, clickAllin theSuperimpose by ASLsection. The superposi- tion is done using the atom numbers. This option is useful if each entry has the same number of atoms and is numbered the same way, which usually requires that the entries be conformers. When you clickAll, 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 theAtom Selection dialog box, but the superposition does not use symmetry in this case.
If the structures you want to compare are not conformers, or if you only want to compare part of the structure, you can select the atoms to superimpose by making a selection in the
Workspace and clicking Selection, or by clickingSelectand using the Atom Selection
dialog box to select the atoms, or by entering the ASL expression in the text box. For example, to use only carbon atoms for the superposition operation, typeatom.e Cand pressENTER. For more information on the Atom Specification Language, see theMae- stro Command Reference Manual.
• Superimpose by SMARTS—To superimpose atoms defined by a SMARTS pattern, you can enter the pattern in the Superimpose by SMARTS text box, or you can create a SMARTS pattern from the atoms that are selected in the Workspace. This method is use- ful if you want to superimpose structures in which the atom numbering of key parts of the molecule is different, such as conformers that do not have the same atom numbering. To select the Workspace atoms and create a SMARTS pattern from them, first use the Workspace selection toolbar button to select the atoms.
Once you have selected the desired atoms, clickGet From Selection. The SMARTS pat- tern corresponding to the selected atoms is entered in theSuperimpose by SMARTStext box.
The default action when superimposing structures is to apply a transformation to the entries, then calculate the RMS difference in coordinates. If you want to preserve the coordinates of the superimposed structures, selectCalculate ‘in place’ (no transformation). The RMS difference is then calculated without moving the structures. This is a convenient way of obtaining RMS differences for ligand poses in a receptor, for example.
If you do not use the calculate in place option, you can separate the superimposed entries by clicking theTile Entriesbutton in the toolbar.
The entries are aligned in a grid, but they are not returned to their original coordinates. You can store the RMS deviation as a property for each entry that was superimposed. To create a property, select Create property before you perform the superposition. The property is labeled RMSDentry-ID orRMSD In Place entry-ID, depending on how you performed the
superposition. The reference entry has a value of zero for this property. The reference entry ID is used for entry-ID in the label. If you change the details of the superposition but do not change the reference entry, the property values are replaced. You can always rename the prop- erty if you want to keep it and perform other superpositions with the same reference entry. See
Figure 9.5. The Sets panel.