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Real-Space Refinement Panel |
Perform real-space refinements to optimize the geometries of side chains, loops, or selected residues. The refinement minimizes a weighted function of the force-field energy and the density fit.
To open the Real-Space Refinement panel, you can:
Click the relevant task button in the Real-space refinement section of the PrimeX panel
There are three choices of real-space refinement tasks. For each task, a different set of controls is displayed in the center of the panel. These sets of controls are described in the following sections. The tasks are:
Specify the grid spacing for the map used in the real-space refinement, in angstroms. For the Refine loops task, this text box is only available under the Manual option for the Build mode. The default is 0.5 for minimization and side-chain refinement, and depends on the mode for loop refinement.
This option allows you to set the B-factors for the atoms that are to be fit in the refinement process. You can enter a value in the text box. For the Refine loops task, this text box is only available under the Manual option for the Build mode. The default B-factor is 20 for minimization and side-chain refinement, and depends on the mode for loop refinement.
The controls for loop refinement consist of a set of options for the build mode, a table that lists the loops, text boxes for the loop limits, a button for loading the loops table from the Workspace structure and an option to bias the loop prediction towards the existing structure.
These options set the grid spacing and the B-factors of the atoms to be refined:
The Loops table lists all the loops, along with the starting and ending residue numbers. To choose a loop for refinement, select the table row. The table columns are described below.
| Feature | Loop label | |
| Chain | Name of the chain in which the loop occurs. | |
| Res1 | First residue in loop. | |
| Res2 | Last residue in loop. |
When you choose a table row, the chain name, and the starting and ending residue numbers are loaded into these text boxes. To change the limits of a loop, change the residue numbers in the Start and End text boxes.
This button reloads the table from the Workspace structure, which is useful when the structure has been replaced or modified.
This option allows you to sample conformational space more heavily around the existing structure, with the result that the refined loop is more likely to resemble the input loop.
The controls for the prediction of side chains consist of a set of standard picking controls, with which you can pick the residues whose side chains are to be refined.
The controls for minimization consist of a set of standard picking controls, with which you can pick the residues to be refined.
This button opens the Calculation Settings dialog box, in which you can set the resolution limits and limits for rejecting reflections; choose an overall B-factor scaling and a bulk solvent correction; choose whether to use implicit solvation, include hydrogen atoms in the output, restrain planar groups, set B-factors for the duration of the job, use phased reflections for the map, and change the relative weight of the force-field and X-ray terms.
The Job toolbar is used to make settings for a job and to start it.
Enter a name for the job in this text box.
This button opens the Job Settings dialog box. The arrow to the right opens a menu, from which you can make settings or perform actions that are related to the job.
The menu items are described below.
This icon indicates when there are jobs running for the application that belong to the current project. It starts spinning when the first job starts, and stops when there are no more jobs running. If a job fails to start, it changes to an exclamation point.
Clicking the button shows a small job status window that lists the job name and status for all active jobs submitted from the current panel (for Jaguar and MacroModel this means all jobs from any of the application panels). You can double-click on a row to open the Monitor panel and monitor the job, or click the Monitor button to open the Monitor panel and close the job status window. The job status is updated while the window is open. If a job finishes while the window is open, the job remains displayed but with the new status. The rows are colored according to the status: yellow for submitted, green for launched, running, or finished, red for incorporated, died, or killed. Click anywhere outside the window to close it.
Run the job with the current job settings.
The status bar displays information about the current job settings for the panel. This includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. It also displays a message for a short time when you start a new job.
The status bar also contains the Help button, which opens the help topic for the panel.
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