Project Table — Shortcut Menus

Shortcut Menu Features

• Entry shortcut menu
• Property shortcut menu
• Entry groups shortcut menu
• Single group shortcut menu
• Surfaces shortcut menu
• Hypotheses shortcut menu
• Trajectory shortcut menu

• Entry
• Property
• Entry groups
• Single group
• Surfaces
• Hypotheses
• Trajectory

Entry shortcut menu

This menu is displayed when you right-click in a cell of the project table, and the actions apply to the selected entries. If you right-click in the Row or the In column, the selection does not change. If you right-click in any other column, what you clicked on is selected before the menu is shown. You can use control-right-click to change the selection of the current row before showing the menu, and shift-right-click to extend the selection to the current row before showing the menu.

Any actions on the selected entries preserve the group hierarchy for fully selected groups.

For menu items that have a complementary item that performs the opposite action (e.g. Include and Exclude), only the item that is relevant to the entry that was right-clicked is shown. If you click in a shortcut row, only the Include/Exclude, Fix in Workspace/Clear Fix, and Lock/Unlock items are shown, along with the items that only apply to shortcut rows.

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.

Property shortcut menu

The property shortcut menu duplicates some items on several of the menus, and has some extra items. This menu is displayed when you right-click in a column header or click on the arrow icon that is displayed when the pointer is in the column header. The actions apply to the property in that column. All menu items are described below.

Hide	Hide this property column.
Sort Selected (ascending)	Sort the selected rows in ascending order.
Sort Selected (descending)	Sort the selected rows in descending order.
Sort All (ascending)	Sort all rows in ascending order.
Sort All (descending)	Sort all rows in descending order.
Color by Property Value	Submenu with the following actions: Show Colors—Check box to show or hide the column colors. Edit Settings—Make or change settings for coloring properties by value. Opens the Edit Color Settings Dialog Box.
Select by Property Value	Select entries based on the values of the property, either from the current selection or from all entries. Opens the Select by Property Value Dialog Box.
Deselect Duplicate Values	Deselect the selected rows in which the property value is the same as that of the first selected entry in the same group. No action is taken on ungrouped entries. This item is only present for string-valued properties, such as the title.
Change Case of Values	Change the case of string-valued properties. This item is present on the Property shortcut menu only if the property values are strings and changes in the value are permitted. You cannot change the case of these properties: Entry ID, Date Added, Date Modified, PDB format version, original cms file, source file, Job Name, ct type. The submenu offers the following choices: lowercase—Change the case of the property values to all lower case. UPPERCASE—Change the case of the property values to all upper case. Title Case—Change the case of the property values to title case, in which first letter in each word is in upper case, and the rest is in lower case.
Fit To	Adjust the width of the column. The submenu offers the following choices: Header—Set the column width to the width of the column heading. Data—Set the column width to the width of the longest data value. Header + Data—Set the column width to the maximum of the heading width and the width of the longest data value.
Move To	Move this property to another location in the table. You can move the property left or right one column, move it to the first or last position in the scrolling section, move it to a position before or after a selected property, or move it between the fixed section and the scrolling section of the table.
Copy Property	Copy values from one property to another, for the selected entries or for all entries. Opens the Copy Property Dialog Box.
Edit Property	Edit Name/Type—Rename the property. You can change the visible name and the internal name, and you can also change the property type. Opens the Change Property Dialog Box. Decimal Places—Set the number of decimal places displayed for one or more real-valued properties. This item is present on the Property shortcut menu only if the property has real values. Opens the Set Decimal Places dialog box. Reorder—Change the order that the properties appear in the Project Table. Opens the Reorder Properties Dialog Box. Clear Values—Clear values of this property for the selected entries.
Delete Property	Delete this property from the project.
Show Property in Workspace	Add or remove the property from the Workspace display. The submenu offers the following choices: Add—Add this property to the properties shown in the Workspace. Replace—Replace the properties shown in the Workspace with this property. Remove—Remove this property from the properties shown in the Workspace.

Entry groups shortcut menu

The entry groups shortcut menu has a number of items that are on the Table menu. It is displayed when you right-click in a group row in a column other than the Row column and In column. The following items are shown, and apply to all selected groups and entries:

Include	Include the selected entries in the Workspace along with the entries that are already included.
Include First Entry	Include in the Workspace the first entry at the top level of each selected group, 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.
Rename	Edit the title of the group that you right-clicked.
Duplicate	Duplicate the group. The duplicate group is placed below the source group. Duplication makes copies of all the entries in the source group and places the copies in the new group.
Delete	Delete the selected entries and groups in the Project Table. The entries and groups are removed from the project.
Ungroup Groups	Move the entries out of the groups, and delete the groups. The entries in each group are placed in the hierarchy where the group was.
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 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.
Collapse	Collapse entry groups in the table, so that only the group title row is visible. The submenu offers the following choices: Selected—Collapse the selected groups, so that only the group titles are visible. Unselected—Collapse the unselected groups, so that only the group titles are visible. All—Collapse all groups, so that only the group titles are visible.
Expand	Expand groups so that their entries are visible in the table. The submenu offers the following choices: To Selected Entries—Expand groups and subgroups that have selected entries so that all these entries are visible. Groups are expanded no further than necessary. Selected—Expand the selected groups to all levels so that all their entries are visible. Unselected—Expand the unselected groups to all levels so that all their entries are visible. All—Expand all groups to all levels.
View Poses	View docked poses in the context of a receptor. You can step through poses, and display interactions with the receptor. Opens the Pose Viewer Panel.

Single group shortcut menu

The single group shortcut menu is displayed if you right-click in the In or the Row column of an entry group row. The menu items apply only to the right-clicked group and the action does not change the entry selection, except for duplicating entries. The items are described below.

Include Group	Include in the Workspace all the entries in the group, along with the entries that are already included.
Include First Entry (Top Group)	Include in the Workspace the first entry at the top level of the group, along with the entries that are already included.
Exclude Group	Exclude all entries in the group from the Workspace.
Invert Entry Selection	Invert the entry selection inside the group.
Select First Level Only	Select all entries at the top level of the group, leaving the selection in any subgroups the same.
Rename	Edit the title of the group that you right-clicked.
Delete	Delete the selected entries and groups in the Project Table. The entries and groups are removed from the project.
Ungroup (Top Groups)	Ungroup the group. The contents of the group are placed at the same level in the hierarchy as the group, and all subgroups are preserved.
Flatten Subgroups	Ungroup all subgroups inside the group to all levels, preserving the group itself.
Duplicate Entries	Duplicate all entries inside the group, without duplicating the group itself. The entries are duplicated in place, i.e. each duplicate is placed after its source entry. The duplicates are selected, and any duplicate whose source was included in the Workspace is included instead of the source.
Collapse	Collapse entries inside the group, so that only the group or subgroup title rows are visible. The submenu offers the following choices: Top Group Only—Hide the entries at the top level of the group, leaving the subgroups as they are. Selected Subgroups—Collapse the selected subgroups, so that only the group titles are visible. Unselected Subgroups—Collapse the unselected subgroups, so that only the group titles are visible. All—Collapse the entire group, so that only the group title is.
Expand	Expand entries inside the group, so that only the group or subgroup title rows are visible. The submenu offers the following choices: Top Group Only—Show the entries at the top level of the group, leaving the subgroups as they are. Selected Subgroups—Expand the selected subgroups, to show all their entries. Unselected Subgroups—Expand the unselected subgroups, to show all their entries. All—Expand the entire group, to show all entries at all levels.

Surfaces shortcut menu

The Surfaces shortcut menu provides control for the display of surfaces. It is displayed when you click or right-click the S in the Title column for an entry, and applies actions to that entry. The menu is divided into two sections. The lower section has a list of the available surfaces for the entry, which you can select for display. The upper section has the following items:

Manage		Open the Surface Manager Panel.
Hide All		Undisplay all surfaces for the entry

Hypotheses shortcut menu

This shortcut menu contains items for the display of Phase hypotheses and actions that you can perform on the hypotheses.

View Hypothesis		Display the hypothesis for the entry in the Workspace.
Quick Screen		Perform a quick screening of the selected entries against the hypothesis.
Next Steps		This submenu offers possible actions to take with the hypothesis. Validate Hypothesis—validate the hypothesis using a set of actives and decoys. Opens the Hypothesis Validation Panel. Add to Database Screen—add the hypothesis to a database screening. Opens the Phase Ligand Screening Panel.
Show		Show or hide objects related to the hypothesis in the Workspace. The objects that are shown have a check mark to the left of the item. Excluded Volumes Manage Excluded Volumes (opens the Manage Excluded Volumes Panel) Feature Labels Feature Tolerances Feature Properties Reference Ligand

Trajectory shortcut menu

The Trajectory shortcut menu provides control for playing trajectories from an MD simulation. It is displayed when you click or right-click the T button in the Title column for an entry. Double-clicking the button loads the trajectory and displays the Trajectory Player. The menu has the following items:

Load Trajectory		Load the trajectory and display the Trajectory Player. Double-clicking the button does the same. If the trajectory is missing (i.e. is not in the same directory as the associated CMS file that was imported into Maestro), a dialog box opens, with three actions: locate the trajectory (Import File) and copy it to the directory that the CMS file is in, renaming if necessary; remove the trajectory data from the entry (Remove Data); or cancel the loading of the trajectory (Cancel).
View Advanced Settings		Open the Advanced Playback Settings Dialog Box. Only available if a trajectory is loaded.
Remove Trajectory Data		Remove the trajectory data stored in the project that indicates a trajectory is available for the entry. The T button is removed. The trajectory itself is not removed, as it is outside the project.