Structure Hierarchy panel

Structure Hierarchy Features

• Structure Hierarchy (Hierarchy)
  • Search button
  • More options button
  • Structure hierarchy
  • Shortcut menus
    • Selected Atoms shortcut menu
    • Selected Entries shortcut menu
    • Selection shortcut menu
• Project information

 

Structure Hierarchy (Hierarchy)

The Structure Hierarchy shows a hierarchical view of the contents of all the entries that are included in the Workspace, classified into components of various types. The classification is shown in a tree, so that you can expand or collapse the tree to show the components that constitute a larger component. For example, a receptor entry may be classified into Protein, Ligands, Solvents, and Other. The protein is divided into chains, which are divided into individual residues. Or an antibody entry can be divided into antibody and antigen, the antibody into light and heavy chains, then into the various regions and finally into residues. Similarly, a GPCR structure can be grouped by GPCR structural regions, including transmembrane helices (TM1-TM7), helix 8 (H8), intracellular loops (ICL), extracellular loops (ECL), and terminal regions.

Each entry in the Workspace is represented as a row in the Structure Hierarchy, with an "All" folder at the top level that contains everything, if there is more than one entry in the Workspace. In addition, there is a row for the current atom selection that functions in the same way as the other components in the hierarchy.

The Structure Hierarchy allows you to work with the structure at each level, offering a visibility toggle, a styling toolbox, and atom selection for each row of the tree.

Search button

The search button displays and hides the search text box, so you can filter the hierarchy on the names. For example, filtering on ARG shows all the arginine residues (and anything else whose name happens to match this text). You can search for multiple items using OR logic by separating them with a | character: for example ARG|LYS searches for ARG or LYS.

To remove the filter, clear the text or use the X button at the right of the search text box.

More Options button

This button menu has settings for configuring the behavior of the structure hierarchy.

• Display Polar H Only—when changing the display of any component, display only the polar hydrogens, rather than all hydrogens, for that component. This is a setting, so it does not change the display immediately, in contrast to the button in the Style toolbox, which acts immediately on the selection.

• Show Annotated Features—toggle on or off to display the annotated features for antibodies. When annotated features are displayed, a check mark is displayed to the left of Show Annotated Features.

• Collapse/expand button—Collapse the Structure Hierarchy so that only the title bar with the buttons is visible. This allows more space for the Entry List. The expand button restores the Structure Hierarchy to its previous size. You can also drag the divider between the Entry List and the Structure Hierarchy to change their relative sizes, or double-click the divider to equalize the sizes.

 

Structure hierarchy

Lists the content of all entries that are in the Workspace (included entries), in a hierarchy that allows you to examine and operate on the various components of the entry, such as chains, residues, ligands, monomers, solvent molecules, and so on. The hierarchy is expanded by default to show the top level for each entry in the Workspace.

Clicking on a row in the hierarchy selects the atoms in the Workspace that belong to the component represented by the row. You can use shift-click and control-click to select multiple rows and therefore select the corresponding atoms in the Workspace. Shift-click adds the atoms from the selected rows to atoms that are already selected—this operates in the same way as selection by any other method.. Nonpolar hydrogens can be excluded from the selection—see Selecting Hydrogen Atoms.

Double-clicking a row fits the atoms represented by the row to the Workspace.

The features of each row are listed below. The presence of some of the features depends on the nature of the structure component that the row represents.

• Visibility check box—Show or hide the atoms in the Workspace for this component. This check box allows you to change what is shown in the Workspace without having to make an atom selection first.

  button	status
  	Displayed. All components are displayed. For lowest items, at least one atom is displayed.
  	Partially Displayed. Component contains both displayed and undisplayed atoms.
  	Undisplayed. None of the atoms in the component are displayed.

• Expand/collapse icon—Expand or collapse the item to show its components. By default, the top-level item for all entries in the Workspace are expanded.
  

• Component icon—Indicates the type of component: protein, ligand, etc.
  
  

• Name—Name of the component or component type. If it is an entry, the name is the entry title. For components of a chain, the chain letter prefixes the name of the component.

• Shortcut menu—Right-clicking on the row displays a shortcut menu that depends on the type of component: if an entry, the Selected Entries menu is shown; if a structure, the Selected Atoms menu is shown.

• Style button—Clicking this button opens the Style toolbox (see Changing Structure Styles). The button is displayed on the right of the row when the pointer is over the row.
  

• Highlighting—The row is highlighted if any atoms in the component are selected in the Workspace. The highlighting is lighter if only some of the atoms are selected; it is darker if all the atoms are selected.

At the top is a separate row for the current atom selection. This row has the same features as other rows (except for the expand/collapse icon), so you can use it for styling the current selection rather than using the Style button on the toolbar. It has its own shortcut menu, the Selection menu, which can be used to operate on the selection.

Shortcut menus

The shortcut menus available in the hierarchy are described below:

Selected Atoms shortcut menu

This shortcut menu opens if the component in the hierarchy is a structure, and applies the action to the atoms in the structure component. The items are:

• Display / Undisplay—Show or hide the selected atoms.
• Style—Open the Style palette to apply a style to the selected atoms.
• Expand to Full Residues—Expand the selection to all atoms in the residues, if some residues are partially selected.
• Expand to Full PDB Chain—Expand the selection to the full PDB chains that are represented in the selection.
• Copy to New Entry—Copy the selected atoms to a new project entry.
• Extract to New Entry—Delete the selected atoms from the current entry and place them in a new entry.
• Rename—Opens the Change Atom Properties dialog to the Residue tab with Chain Name enabled, allowing you to rename the selected chains.
• Delete Atoms—Delete the selected atoms.

Selected Entries shortcut menu

This shortcut menu opens if the component in the hierarchy is an entry. The items are:

Include	Include the selected entries in the Workspace along with the entries that are already included.
Exclude	Exclude (remove) the selected entries from the Workspace. Fixed entries are also removed with this command.
Fix in Workspace	Include the selected entries in the Workspace, and keep them in the Workspace until explicitly excluded or unfixed, the Workspace is cleared, or the project is closed. Actions that exclude other entries from the Workspace, such as Include Only, have no effect on the fixed entries. A pin icon appears in the In column for these entries.
Clear Fix	Change any fixed entries in the entry selection so that they are no longer fixed. The entries remain in the Workspace, but can be removed by actions like Include Only. The padlock icon is removed from the In column for these entries.
Lock (set non-editable)	Lock the selected entries so that they cannot be modified or deleted until they are unlocked. A padlock icon appears in the Row column for these entries. When you include locked entries in the Workspace, a banner is displayed to notify you of their presence. Locked entries cannot be modified in the Workspace.
Unlock (set editable)	Unlock the selected entries so that they can be modified or deleted. The padlock icon is removed from the Row column for these entries.
Split	Split the entry into several entries based on the content. The submenu offers the following choices: By Molecule—Split the selected entry into a set of entries, one for each molecule in the source entry. By Chain—Split the selected entry into a set of entries, one for each chain in the source entry. Into Ligands, Water, Other—Split the selected entry into a set of entries, one for each ligand in the source entry, one for the waters, and one for any other atoms, such as a protein. Copy Properties—Copy the properties of the source entry to the new entries when the source is split.
Duplicate	Submenu with the following actions: In Place—Duplicate the selected entries and place each new entry immediately below its source entry. Into New Group—Duplicate the selected entries and place the entries into a new group. Opens the New Group dialog box, in which you can give the group a title and choose a location for the new group, either at the top level or in a parent group of the selection. Into Existing Group—Duplicate the selected entries and place the entries into an existing group, at the end of the group. Opens the Duplicate into Group dialog box, in which you can choose the group for the duplicated entries. As Ungrouped Entries—Duplicate the selected entries and place the entries at the end of the table. Copy Properties—Select this option if you want to copy the properties of the source entries to the target entries when duplicating entries; deselect it to copy only the structure.
Merge	Merge the selected entries into a single entry. The merged entry is placed after the last selected entry, inside the last entry's entry group if one exists.
Delete	Delete the selected entries and groups in the Project Table. The entries and groups are removed from the project.
Add to Shortcut Rows	Add a shortcut for each selected entry to the shortcut row section. The shortcuts are placed at the top of the table in the fixed area, so they are always visible in the table. Shortcuts are synchronized with the source entries.
Color Row	Color the rows in the Project Table for the selected entries. Opens the Color Rows dialog box which has the following options: No Coloring—Reset the background color for the selected entries to the default color. Constant Color—Color the background of the entire row for the selected entries with a chosen color. Opens a color selector, in which you can choose the color to apply to the rows. The color is stored in the project, associated with the entries that are colored. By Entry Property—Color table cells based on ranges of property values. Click the button to select the property. When you click OK, the Edit Color Settings Dialog Box opens, in which you can define the property ranges and select and apply the colors.
Set Stars	Mark the selected entries with the number of stars chosen from this submenu. The star rating is displayed in the Stars column to set the number of stars for a single entry. The submenu offers the following choices: None—Set the number of stars for the selected entries to 0. 1 (*)—Set the number of stars for the selected entries to 1. 2 (**)—Set the number of stars for the selected entries to 1. 3 (***)—Set the number of stars for the selected entries to 3.
Group	Group the selected entries and groups into a new group. Opens the Group Selected Entries & Groups dialog box, in which you can specify the title of the new group and choose the location of the new group. The group can be placed at the top level, with a choice of locations (top, end, at first or last selected row), or in any common parent group in the hierarchy.
Move to	Move the selected entries so that the first entry is at a specified location. Submenu with the following options: Existing Group—Move the entries to the end of a specified group. Opens a dialog box in which you can select the group. Top of Table—Move the entries to the top of the Project Table, ungrouped. End of Table—Move the entries to the end of the Project Table, ungrouped. Top of Group—Move the entries to the top of the group they are currently in. The entries must be in the same group. End of Group—Move the entries to the end of the group they are currently in. The entries must be in the same group. Top of Parent Group—Move the entries to the top of the group above the groups the entries are currently in (move them up one level in the hierarchy). All entries must share this parent group. End of Parent Group—Move the entries to the end of the group above the groups the entries are currently in (move them up one level in the hierarchy). All entries must share this parent group. Other—Opens the Move to Row dialog box, in which you can specify a row number or move the entries to the first or the last row.
Ungroup Groups	Remove the grouping for any fully selected groups. The entries are placed in the same location in the hierarchy as the groups they were in.
Change Property Value	Set the value of the property in the cell you clicked in. The cell is placed in edit mode (the same as double-click). Only present if a single row is selected.
Set Property	Set the value of the property in the column you clicked in to a specified value. Opens the Set Property for Selected Entries dialog box, where you can specify the value and choose whether to apply it to the clicked entry or to all selected entries. The value in the cell you clicked in populates the text box for the value, which you can then change. Only present if multiple rows are selected.
Manage Entry Properties	Copy properties from a selected entry to the clipboard; paste properties to selected entries, clear property values. Only one entry should be selected for copying, but multiple entries can be selected for pasting or clearing. This submenu is for managing properties within Maestro. To copy entry property values for external use, use the context menu in the Project Table — Property Tree Panel. Submenu with the following options: Copy All Values—Copy all entry properties to the clipboard for pasting into other entries. Copy Column Values Only—Copy the entry properties that are shown (the visible columns) in the Project Table to the clipboard, for pasting into other entries. Paste Values—Paste the property values from the clipboard into the selected entries. The existing properties are overwritten. If a property does not exist (or is of a different type) a new property is created for those entries. If a property value is empty in the source entry, the value will be empty in the target entries. Clear All Values—Clear all property values in the selected entries. Clear Column Values Only—Clear all property values for the properties that are shown (the visible columns) in the selected entries. Choose Properties to Clear—Choose the property values to clear. Opens the Clear Property Values Dialog Box for choosing the properties for which to clear values.
Group by Entry Property	Group the selected entries by the value of a property. Groups are created by property range for numerical property values, and for each unique value for string property values. Opens the Group By Entry Property Panel.
Scroll Table to Row	Scroll the Project Table to the source row for the shortcut row you clicked on. Only present when you click in a shortcut row.
Remove Shortcut	Remove the shortcuts for the selected entries. Only present when you click in a shortcut row.
Style	Apply a display style to the atoms in the selected entries. Displays the Style Toolbox (without the ribbon properties), where you can choose the style to apply.
Export	Export data from the selected entries to external files. The submenu offers the following choices: Structures—Export entries from the current project to one or more files, with a choice of file formats and options to control the export behavior. You can create new structure files or append to an existing structure file. Opens the Export Dialog Box. Spreadsheet—Export rows and columns from the Project Table to a CSV file, which can be read into a spreadsheet application. Opens the Export Spreadsheet Panel. To LiveDesign—Export the selected entries to a LiveDesign project. Opens the Maestro to LiveDesign Export Panel (after authentication, if necessary) with the structure source set to the selected entries.
Apply Annotations	Apply annotations to the selected entries, with options for Antibody or T-Cell Receptor. Selecting Antibody opens a dialog with options to select from the following numberring schemes: Kabat, Chothia, EnchancedChothia, IMGT, and AHo. Selecting T-Cell Receptor opens a dialog with options to apply IMGT or AHo numbering schemes.

Selection shortcut menu

This shortcut menu opens from the Selection row, and applies the action to the selected atoms. The items are:

• Undisplay—Hide the selected atoms.
• Style—Open the Style palette to apply a style to the selected atoms.
• Expand to Full Residues—Expand the selection to all atoms in the residues, if some residues are partially selected.
• Expand to Full PDB Chain—Expand the selection to the full PDB chains that are represented in the selection.
• Select Entries in Table—Select the entries in the Project Table that contain the selected atoms.
• Exclude Entries—Exclude the entries that contain the selected atoms from the Workspace.
• Copy to New Entry—Copy the selected atoms to a new project entry.
• Extract to New Entry—Delete the selected atoms from the current entry and place them in a new entry.
• Save as Custom Set—Generate a custom atom set from the selection. Opens the Save Selection as Custom Set Dialog Box.
• Quick Save (within session)—Save the selection as the next one of the numbered selections.
• Restore Quick Save—Change the selection to the chosen numbered selection.
• Rename—Opens the Change Atom Properties dialog to the Residue tab with Chain Name enabled, allowing you to rename the selected chains.
• Delete Atoms—Delete the selected atoms.

Project information

This area shows information on the entries and entry groups that are present in the project, which filter (if any) has been applied to the entry list, and how many entries are shown in the entry list after filtering.

Related Topics

• Project Table Panel
• Preferences Panel
• Select Entries by Property Values Dialog Box