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 this panel, click Create Map in the PrimeX Panel.

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. For information on command usage and options, see primex Command Help and Running PrimeX Tasks from the Command Line.

  • Features
  • Additional Resources

Create Map Panel Features

 

The features on the left side of the panel provide choices of the type of map and the data that will be used for the map.The right side of the panel contains options for setting up the map. These options are synchronized with those in the Reciprocal-Space Refinement Panel.

Map source options

These options specify the source of the phases used to generate the map.

Observed amplitudes and phases calculated from model option

With this option, phases are calculated from the model. This is the default option.

Amplitudes and phases from file option, text box and Browse button

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.

Map type options

These options allow you to choose the type of map to generate. They are not available if you are reading phases from a file.

Regular map

Create a full density or density difference map, according to the selection in the lower portion of the panel. This is the default map, and the only kind of map that can be automatically generated following a refinement job.

Omit map

Create a map in which selected atoms are omitted. When you select the option, the Select atoms to omitpicking controls and the Omit map type options become available. You can then pick the atoms to be omitted.

Composite omit map

Create 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.

Omit map type options

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 [[15]]. 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. The maximum distance that an atom can move is √3 times the value set in the text box.

Coefficients options

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.

Weighting options

The two options are SigmaA (see Ref. 1) and Unweighted. These options are synchronized with those in the Mapstab of the Reciprocal-Space Refinement Panel. These options are not available if you are reading phases from a file. If you are using the maximum likelihood target, you can specify the weighting model used. If you are using least squares as the target, you can only create an unweighted map.

Grid size options

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.

Scale map to sigma units option

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.

Extent options

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:

    Fractional space
    Define the map as a fraction of the unit cell parameters. The fractional values can be entered in the min and max text boxes for each crystallographic direction.
    Orthogonal space
    Define the extent of the map in Cartesian (x, y, z) coordinates. The coordinate origin is that of the structure in the Workspace.
Calculation settings button

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.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Create Map - 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. You can also reset the panel from the Job toolbar.

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.

Quick Reference Sheets

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