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Prime —Structure Prediction Panel |
The steps in the Structure Prediction panel have many elements in common and share a standard layout. This topic discusses these common elements, their location, and their function.
To open the Structure Prediction panel, you can:
Choose Applications → Prime → Homology Modeling or Tasks → Homology Modeling, then click the Structure Prediction Wizard button in the Homology Modeling panel.
You can bypass the Homology Modeling panel interface by selecting the option Make selection the default and do not show this panel again before clicking the button.
Choose Applications → BioLuminate → Homology Modeling → Advanced Homology Modeling in the main window.
Choose Tasks → Biologics → Homology Modeling → Advanced Homology Modeling in the main window.
In the upper part of the panel is the menu bar, and beneath that, the toolbar. Below the toolbar is the sequence viewer.
As well as displaying sequences for the query and for templates, in some steps, the sequence viewer shows secondary structure predictions (SSP). Right-click on an SSP for a menu of commands that includes Hide All, Delete, and Export. Right-clicking on a sequence also produces a menu of commands appropriate to the current step. Sequences can be exported by choosing Export Sequences from the File menu. You can select residues in the sequence viewer with the mouse: click to select a single residue, shift-click to select a range of residues, and control-click to select or deselect a residue without affecting the selection of other residues. You can also drag to select residues within a row.
The sequence viewer can be configured to display a single line for the sequence that can be scrolled horizontally, or the sequence can be wrapped so that it scrolls vertically. The configuration is controlled by the Wrap Sequences option on the sequence viewer shortcut menu.
If you want to save an image of the sequence viewer, choose Save Image from the sequence viewer shortcut menu. A file selector opens, in which you can select a format, from PNG, TIFF, and JPEG, and save the image.
The icon on the job status button at the upper right of the panel spins when a job is running. When the job has finished, the icon turns to an exclamation point while the job is incorporating, then returns to its original state when the incorporation has finished. You can click the button to open the Monitor panel and monitor the job.
In the center of the panel is the Step View, which shows the step name and a description, a row of action buttons, and data relevant to the step, usually in table format. In the Build Structure step, the Step View also contains output from the Build Structure job's log file.
Tables have the following features:
Beneath the Step View are the Back and Next buttons, which are the primary means of navigation between steps.
The Guide, in the section beneath the Back and Next buttons, is a diagram of the Prime workflow as a series of steps, each step represented by a button. The Guide is both a map display, highlighting your current location, and a navigation tool. It is hidden by default, and can be displayed from the Step menu. For information about the Guide and navigating in Prime, see Prime Navigation and the Guide.
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