Hypothesis Alignment Panel
Align one or more pharmacophore hypotheses to a reference hypothesis.
To open this panel: click the Tasks button and browse to Structure Alignment → Hypothesis Alignment.
- Using
- Features
- Additional Resources
Using the Hypothesis Alignment Panel
Alignments are performed with the align_hypoPair Command Help utility. The alignment requires at least three features to match between the hypotheses.
The transformation that aligns the hypothesis to the reference is also applied to the reference ligand, if there is one, and any other ligands that are in a subgroup of the hypothesis (such as actives or inactives).
Hypothesis Alignment Panel Features
Auto tab
Perform an automatic alignment of a set of hypotheses to a reference hypothesis. The hypotheses to be aligned and the reference hypothesis must all be selected in the Entry List (or Project Table). The hypothesis with the lowest row number (highest in the Entry List) is the reference hypothesis. If you want to align to one of the other hypotheses, you must move it up in the Entry List to the highest position.
The alignment is performed by matching all combinations of features (specific instances of a feature type, also called "sites") in a hypothesis with features in the reference hypothesis, to find the best match. Features are only allowed to match other features of the same type (donor, acceptor, etc.). The alignment is done for the greatest number of features that match and the smallest RMSD for this number of features. If a match cannot be found with the minimum number of features, no alignment is performed for the hypothesis.
- Feature matching tolerance text box
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Specify the tolerance for matching a feature in the current hypothesis with a feature in the reference hypothesis. Features that are inside this distance of each other are considered to match.
- Minimum number of matching features text box
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Specify the minimum number of features that must match in order to perform an alignment. The number of matching features is increased from this minimum to find the greatest number of features that match. This number of features is then used for the alignment. The minimum must not be less than 3, otherwise a unique alignment cannot be found, and the alignment fails.
- Create RMSD property option
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Create a property that records the RMSD between the features of the hypothesis that were used in the alignment and those of the reference hypothesis.
- Align Selected Hypotheses button
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Perform the alignment. The progress of the alignment is displayed in a dialog box.
Feature Pairs tab
Superimpose two hypotheses by picking the pairs of features that must be superimposed. In each pair, one feature must be from the Fixed (reference) hypothesis, and the other from the Free hypothesis (the one that is to be moved into alignment). Both hypotheses must be displayed in the Workspace. You must pick at least 3 pairs, to ensure that a unique alignment is defined.
- Superimpose by feature pairs table
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This table contains the list of pairs of features that are to be superimposed. Initially the table is empty, and rows are added by picking feature pairs in the Workspace. The Fixed column shows the feature picked in the reference hypothesis, and the Free column shows the corresponding feature picked in the hypothesis to be aligned. You can select rows to delete from the table, if for example you decide you do not want to superimpose these two features.
- Delete and Delete All buttons
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Delete the selected rows from the table, or delete all rows from the table to start over.
- Pick features in Workspace option
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Select this option to pick the feature pairs in the Workspace that are to be superimposed. The first pick for each pair must be in the Fixed hypothesis, the second must be in the Free hypothesis. You must pick at least three feature pairs.
- Create RMSD property option
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Create a property that records the RMSD between the features of the hypothesis and those of the reference hypothesis. The RMSD only includes features that were used in the alignment.
- Superimpose Feature Pairs button
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Perform the alignment.