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 this panel, click Water Placement in the PrimeX panel.
- Using
- Features
- Additional Resources
Using the Water Placement 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.
To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write.
Water Placement Panel Features
- Minimum peak height (Fo-Fc) text box
- Maximum B-factor text box
- Minimum hydrogen-bonding distance text box
- Minimum distance to other atoms text box
- Maximum distance to other atoms text box
- Calculation Settings button
- Job toolbar
- Status bar
- Minimum peak height (Fo-Fc) text box
-
Specify the minimum height of any peak that will be used to place a water molecule.
- Maximum B-factor text box
-
Specify the maximum B-factor for any water molecule to be accepted as placed. Water molecules with larger B-factors are rejected as "noise".
- Minimum hydrogen-bonding distance text box
-
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.
- Minimum distance to other atoms text box
-
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.
- Maximum distance to other atoms text box
-
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.
- Calculation Settings button
-
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.
- Job toolbar
-
Manage job submission and settings. See Job Toolbar for a description of this toolbar.
The Job Settings button opens the Water Placement - Job Settings Dialog Box, where you can make settings for running the job.
- Status bar
-
The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.
Use the Reset button
to reset the panel to its default settings and clear any data from the panel. The status bar also contains the Help button
, which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a 
button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.