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Manage Surfaces Panel |
Manage the surfaces associated with project entries. This includes selecting surfaces to display, setting parameters for the appearance and display of surfaces, importing and exporting surfaces, and deleting surfaces.
To open the Manage Surfaces panel, you can:
Choose Workspace → Surface → Manage Surfaces in the main window.
Choose Manage from the Surfaces button menu on the Style toolbar.
To open the Manage Surfaces panel with the data for a project entry displayed, click the S button in the entry row in the Entry List panel or in the Title column for the entry in the Project Table.
The Surface Table consists of the following columns:
Displays or undisplays the surface for that entry in the Workspace. You can use shift-click to display multiple surfaces in the Workspace, and you can use control-click or middle-click to display or undisplay individual surfaces.
If limits are set for this entry, a checkbox is displayed. You can then click in the box to turn limits on or off. To add or edit limits, click the Limit button.
Lists the entry ID and the title of the entry that contains the surface.
Lists the name of the volume from which the isosurface was created.
Displays or undisplays the volume for that entry in the Workspace. You can use shift-click to display multiple volumes in the Workspace, and you can use control-click or middle-click to display or undisplay individual volumes. Volume display can be set up in the Volume Color Map Editor panel.
Edit this field to create a unique surface name within each entry.
Edit this field to add your own comments. Jaguar fills this field in with molecular orbital information.
Lists the type of surface to be displayed: molecular surface, Van der Waals, extended radius, density, potential, orbital, spin, hydrophobic, or hydrophilic.
Lists the value that was used to create the surface. To change this value, use the Isovalue slider at the bottom of the panel or enter a value in the text box next to it. For regular surfaces, this field is blank.
Lists the surface area of the limited surface (summation of all polygons).
(PrimeX only) Sigma value used to generate the map.
You can select rows in the table with the usual click, shift-click and control-click. With the exception of Import, the buttons below the table act only on the selected rows.
Right-clicking and holding in the surface table opens a shortcut menu from which you can change the surface color (constant color and color by property), style, and transparency, for the selected rows. For a fuller description of the options, see the Surface Display Options Dialog Box topic.
The Surface Table panel buttons perform the following actions:
To import a surface or volume, click Import to open the Import Surface/Volume dialog box. Navigate to a file, select it and click Import. The Choose Entry dialog box opens, so that you can choose the entry you want associated with the surface or volume. Select the desired entry and click Choose. The surface is imported and attached to the chosen entry.
Click to duplicate the selected surface. A new surface is created with "1" appended to the surface name.
Click to delete the selected volume or surface. If more than one item is selected, all of the selected items are deleted.
Split surfaces that have both positive and negative values into two
surfaces: one for the positive values and one for the negative values. The
original surface is retained, and two new surfaces are created, with suffixes
_positive and _negative. This button acts on the
selected surfaces, and is only available if all selected surfaces are paired
(have both positive and negative surfaces).
Opens the Limit Surface panel. This panel allows you to control how much of the surface is displayed by selecting atoms and a distance from those atoms to define a boundary for the surface.
Exports the volume data associated with the selected surface to a formatted or unformatted CNS or CCP4 map file. Available only when a single surface is selected. Opens a file selector that allows you to browse to a location and name the file.
Opens the Display Options panel. This panel allows you to control how the surface is displayed by selecting the transparency, style, and color scheme of the surface.
Opens the Volume Color Map Editor panel. This panel allows you to set the color and opacity values as a function of data value for displaying a volume.
Opens the Preferences panel at the Surfaces – Performance settings.
The Isovalue slider changes the value of the volume data for which the surface is computed, and therefore changes the extent of the surface. Larger values usually mean smaller surfaces. The isovalue is applied only to the selected surface, and is unavailable unless only one surface is selected. You can also enter a value directly into the text box to the right of the slider. For PrimeX, the fraction of Sigma is also displayed.
In the Display at most text box, you can specify a cubic volume that is used to limit the surface display. The cube can be centered on an atom by spot-centering on that atom (right-click on the atom) or on a residue by selecting a residue in the sequence viewer with the middle mouse button. For PrimeX, it is automatically centered on the center of the map, and can be centered by selecting atoms and choosing Center Electron Density from the shortcut menu in the Workspace.
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