|
|
Reciprocal-Space Refinement Panel |
Perform reciprocal space refinements. These can include minimization of R-factors for the coordinates, B-factors and grouped occupancies; adjustment of parts or all of the protein as rigid bodies, and simulated annealing.
To open the Reciprocal-Space Refinement panel, you can:
Click the relevant task button in the Reciprocal-space refinement section of the PrimeX panel
Often, the first step in a refinement is the overall positioning of the protein, which is done by treating the protein as a rigid body. PrimeX provides the means to define multiple rigid bodies for the refinement. To perform a rigid-body refinement, choose Rigid body from the Refinement method option menu. This method is usually used with only the low-resolution data. You might therefore increase the high resolution cutoff for the reflection data in the Calculation Settings dialog box.
Simulated annealing is generally used the middle stages of the refinement, after the larger changes in positions have been completed with rigid-body and real-space refinement. Usually the initial temperature is decreased with successive runs.
Minimization is usually done in the last stages of the refinement. This method is often the best for placement of water molecules.
After each refinement job is done, maps are automatically generated. You can select the type of map and set up the parameters of the map in the Maps tab.
There are three refinement methods available:
Minimize the R factors for the coordinates, B-factors, and grouped occupancies. Useful for water placement and small changes to coordinates.
Adjust the overall positioning of the protein by moving it or user-defined pieces as rigid bodies. Usually used at the beginning of a refinement with only the low-resolution data.
Perform a simulated annealing calculation. Useful for moving across low energy barriers.
There are four tabs, which contain controls for the refinement. Three of these are common to all refinement methods. The fourth tab changes according to the method chosen. The tabs are described in separate topics:
This button opens the Calculation Settings dialog box, in which you can set the resolution limit, overall B-factor scaling, choose a bulk solvent correction, set limits for rejecting reflections, and choose whether to include hydrogen atoms in the output.
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.
|