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Create Map Panel |
In the Create Map panel, you can set up and run a job to create various types of electron density maps.
To open the Create Map panel, you can:
Click Create Map in the PrimeX panel.
These options specify the source of the phases used to generate the map.
With this option, phases are calculated from the model. This is the default option.
With this option, phases are obtained from a file that contains phased reflections. When you select this option, the Browse button becomes available, and you can enter the file name in the text box or click Browse and navigate to the file in a file chooser.
These options allow you to choose the type of map to generate. They are not available if you are reading phases from a file.
This is the default.
This option creates a map in which selected atoms are omitted. When you select the option, the Select atoms to omit picking controls and the Omit map type options become available. You can then pick the atoms to be omitted.
This option creates a map constructed by systematically omitting a percentage of atoms. When you select this option, the Data to omit text box becomes available, and you can enter the percentage of atoms to omit.
If you select an omit map, two omit map types are available:
Basic—This is the default type, in which atoms are simply omitted.
Kicked—In this map type, the atoms remaining after deletion are displaced randomly, and the displacement is done several times and the maps are averaged to generate a final map.You can specify the maximum displacement along any axis in the Maximum displacement text box and the number of maps that are generated by "kicking" and averaged to obtain the final map in the Number averaged text box.
Four options are provided for the coefficients to be used in the map: Fo, Fo-Fc (difference map), 2Fo-Fc, and 3Fo-2Fc. You can select any number of these options to create multiple maps. If you read amplitudes and phases from file, an Fo map calculation is implied since the amplitudes from the file are used without modification.
The two options are SigmaA and Unweighted. These options are synchronized with those in the Maps tab of the Reciprocal-Space Refinement panel. These options are not available if you are reading phases from a file.
Two preset options for the grid spacing are provided: 0.33 Å, 0.25 Å. If you want to specify your own grid spacing, select Other and enter a value in the text box. These options are synchronized with those in the Maps tab of the Reciprocal-Space Refinement panel.
This option allows you to scale the map to sigma units, instead of the default units. If you are reading phases from a file, this option is off by default.
The Extent options allow you to specify the extent of the map. These options are synchronized with those in the Maps tab of the Reciprocal-Space Refinement panel. There are four options:
Molecule, plus N Å — Limit the map to the region within the specified distance of the structure in the Workspace.
Unit cell — Calculate the map for the entire unit cell.
Asymmetric unit — Calculate the map for the asymmetric unit.
Box — Calculate the map for the box defined in the text boxes. There are two options for the box:
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. You can also open the Set Default Map Color dialog box to set the default colors for each map type.
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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