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Water Placement Panel |
In this panel you set options and run a job to place water molecules. The options in this panel ensure that water molecules are placed in reasonable locations.
To open the Water Placement panel, you can:
Click Water Placement in the PrimeX panel.
To place water molecules, you must first have a difference density map. Water molecules are placed in all locations that match the criteria specified in the text boxes. When you have set these values, choose Job Settings from the Settings button menu,
set the job parameters in the Job Settings dialog box, and click Run to run the job.
Once the job is run, it is a good idea to check the placements using the Density Fit panel.
To center the view on a particular part of a density map, right-click on one of the displayed vertices of the map.
Specify the minimum height of any peak that will be used to place a water molecule.
Specify the maximum B-factor for any water molecule to be accepted as placed. Water molecules with larger B-factors are rejected as "noise".
Specify the minimum distance between the oxygen atom and a hydrogen-bond donor or acceptor. Water molecules will not be placed in locations where this distance is less than the value specified.
Specify the minimum distance between the oxygen atom and any other atom. Water molecules will not be placed in locations where this distance is less than the value specified.
Specify the maximum distance between the oxygen atom and any other atom. Water molecules will not be placed in locations where this distance is greater than the value specified.
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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