Consensus Visualization Panel
In this panel, you can identify structural elements, such as ligands, waters, or counter ions, that are in the same position in a set of related proteins.
To open this panel, click the Tasks button and browse to Biologics → Consensus Viewer.
- Using
- Features
- Additional Resources
Using the Consensus Visualization Panel
This panel is intended for use to identify common structural elements in set of related proteins, which you might want to do at the beginning of a project, for example. After importing the proteins you can then align them structurally and then look for structural entities such as ligands, waters, and counter ions that are in the same region in all or a consensus of the structures. The consensus can help you identify different binding modes of the ligands, structural waters, and salt bridges. The identity of any consensus molecule can be ascertained by moving the pointer over the structure in the Workspace and viewing the text in the status bar, below the Workspace.
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Import the protein that you are interested in.
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Import related proteins.
You can run a BLAST search to find homologs by selecting the protein in the sequence viewer and clicking Find and Align Homologs, or import the other proteins, which can be proteins from the same family, or the same protein with different ligands, or different crystal structures of the same protein, for example. You do not usually need to change the BLAST search settings.
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Structurally align the proteins.
If they are already aligned, you can skip this step. Otherwise, you can align them by clicking Align. All the proteins you imported are aligned.
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If you want to view the results of a consensus, specify the percentage or the number of proteins that constitutes a consensus, with the Define consensus options and text boxes.
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Set display options
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Examine the locations of waters, counter ions, or ligands in the Workspace using the tools in the lower part of the panel, or display protein residues near these objects. You can display or undisplay proteins with the check boxes to the left of their names in the sequence viewer.
If you choose to prepare the protein beforehand in the Protein Preparation Workflow Panel, you should ensure that you do not delete any of the molecules for which you are seeking a consensus. In particular, you might want to deselect Delete waters beyond hets in the Preparation Workflow tab, or make the distance large enough to ensure that you have the relevant waters.
Consensus Visualization Panel Features
- Import button
- Find pattern tools
- Sequence viewer
- Find and Align Homologs button
- Align button
- Define consensus options and text boxes
- Water section
- Counterion section
- Ligand section
- Import button
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Import structures for the consensus visualization. The choices are:
- Browse for File—Open a file selector to select a Maestro or PDB file that contains a protein structure.
- PDB ID—Import a protein from the PDB. Opens a dialog box in which you can specify the PDB ID.
- From Workspace—Import the protein that is in the Workspace.
- Find pattern tools
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Find a particular pattern in a sequence. You can use an extended PROSITE syntax, which makes use of secondary structure and property information; the syntax is explained in the tooltip. See the Multiple Sequence Viewer/Editor — Toolbar topic for more information.
- Sequence viewer
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Displays the sequences. The names are in the left pane, along with the names of the annotations. The check box to the left of the name is for displaying or undisplaying the protein in the Workspace. The shortcut menu allows you to move the sequence, select sequences, and clear annotations. The sequence is in the right pane. You can select residues, color residues with various schemes, and show annotations for the sequence from the shortcut menu.
- Find and Align Homologs button
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Run a BLAST search to find homologs to the reference sequence. Opens the BLAST Search Settings dialog box, in which you can make settings and then start the job. While the job is running, the progress is displayed in a dialog box that also allows you to cancel the job. When it finishes, the BLAST Search Results dialog box opens. You can then select the homologs you want to use for the alignment. These homologs are aligned with the protein structure alignment tool.
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The structures are imported without any preprocessing, so they might have structural defects. For the purposes of this panel, it is generally acceptable to use structures from the PDB that have structural issues. If an information box opens stating that problems were found when importing a structure, you can select Do not show this dialog again to prevent it from opening for each structure that has problems, and click OK.
- Align button
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Align all the protein structures using the protein structure alignment tool. This tool uses an algorithm that attempts to align secondary structure elements as it aligns the protein structures.
- Define consensus options and text boxes
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Select one of these options to define the consensus, either in terms of a percentage of structures or a number of structures. A consensus on a particular structural element (such as a water) is obtained when the element is within 2 Å of the same location in the specified number or percentage of structures.
- Water, Counterion, and Ligand sections
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These sections allow you to choose structural objects (water, counterions, ligand) to display in the Workspace, the residues to display near these structural objects, and the color to be used for these objects. The controls are the same for each structural object. Waters and ions are displayed in sphere representation, ligands are displayed in ball-and-stick representation. Consensus objects are highlighted with a silhouette. (You can change the highlight style in the Manage Highlights Panel).
You can control which proteins are displayed in the Workspace from the Sequence Viewer.
- Display option menu
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Choose whether to display all, only the consensus, or none of the particular structural object. For example, viewing all the molecules gives an indication of whether a consensus exists, whereas viewing the consensus shows whether there is a strong enough consensus to consider the molecule as conserved.
- Select and display residues near option menu
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Select and display the protein residues that are near (within 5 Å) any of the particular structural objects or only the consensus structural objects, as chosen from the option menu. The action is not performed until you click Select.
- Color button
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Choose the color to apply to the structural objects that are displayed. When you click the button, a color selector opens, so you can choose the color. The chosen color is displayed on the button.
- Select button
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Select the residues that are within 5 Å of the structural objects as defined by the option menu. The residues are selected in the Workspace and colored with the color shown on the color button.