2D Viewer Panel

The 2D viewer allows you to display 2D structures for entries in the Project Table in a tiled view. It provides tools for displaying properties, annotating structures with properties, alignment of the 2D structures, and selection and inclusion of entries.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Structure Analysis → 2D Viewer
  • Click the Tasks button and browse to Project Table and Project Operations → Open 2D Viewer
  • In the Project Table panel, choose Window → Open 2D Viewer
  • Click the gadgets menu button,

    then click the 2D Viewer icon.
  • Using
  • Features
  • Additional Resources

Using the 2D Viewer Panel

The basic function of the 2D Viewer panel is to display 2D representations of the structures in the Project Table and their properties, provide capabilities for aligning the 2D structures and selection and inclusion of the entries, and export of the structures and properties.

The 2D structures are laid out in a grid by default, with one structure and its selected properties in each tile.

The 2D structures are images that are created when the panel is opened, or when you click Reload to update the panel contents from the Project Table. Images are not created for proteins or other large structures, but if a protein has a ligand, the ligand structure is drawn, and an icon is displayed in the top right corner to indicate that the structure contains a protein.

The 2D structures can be aligned to one of them (the reference) by use of their maximum common substructure. The structures can all be flipped horizontally or vertically, and rotated in increments of 15°.

In addition to the structures, properties can be displayed in a list below the structures in each cell. Real properties are displayed to the same precision as in the Project Table. To select properties to display and set the order in which they are listed, choose Change view → Manage Entry Properties.

You can also display an atom-level property for each atom instead of the atomic symbol. To select the property, choose Change view → Choose Atom Property.

Tiles can be selected for an action. The selection has no relation to selection in the Project Table, but you can alter the selection or inclusion state of a structure from the shortcut menu in a tile, and perform other operations.

The inclusion state is always the same as in the Project Table, and is indicated by the circle in the top left of each cell. You can automatically include in the Workspace the structures that you select in the panel by selecting Change view → Link 2D Selection and Inclusion. With this option, whenever you select a tile, the structure is included in the Workspace. Selecting multiple tiles includes all the structures in the Workspace.

2D Viewer Panel Features

 

Get structures from option menu

Choose the source of the structures to display in the viewer, from Workspace, Selected entries, All entries. When you have made a choice, you can press Enter to load the structures, or click the Reload button.

Reload button

Reload the structures in the viewer from the structure source. The previous set is cleared and replaced with the new set. This allows you to change the selection or inclusion and choose whether to update the set of structures in the viewer.

This button is not available if Auto-update is selected.

Auto-update option

Update the viewer automatically when the selection or inclusion changes. The previous set of structures is cleared and replaced with the new set. This option provides immediate response to any changes.

Reference option menu

Specify a reference structure for alignment of the 2D structures in the panel. For congeneric series it is useful to see all the structures in the same orientation. The 2D image of the reference structure is updated to match the orientation of the 3D structure in the Workspace, and is highlighted in light blue. If structures were aligned to a previous reference, the 2D image reverts to the default and is no longer highlighted. If you choose None after previously choosing a reference structure, the reference highlighting is removed, but any alignment of other structures is retained.

Align All button

Align all other structures to the reference structure, so that they appear in the same orientation. The alignment is performed using the maximum common substructure (MCS) of each structure with the reference structure. The alignment only works for congeneric structures: if no common substructure is found (or it is too small), no alignment is done. You can view the MCS for the aligned structures by choosing Change view → Highlight Aligned Substructures.

More Actions option
Optionally transform all 2D structures buttons

These buttons allow you to adjust the orientation of all the 2D structures together.

Rotate all structures anticlockwise by 15°.
Rotate all structures clockwise by 15°.
Flip all structures horizontally.
Flip all structures vertically.
Export options

Export the selected structures or all structures as images or to structure files. The menu has the following items:

  • Save Individual Images—save individual images as PNG or SVG files. See 2D Viewer - Save Individual Images.

  • Save a Single Grid Image—save a single image of the grid as a PNG, HTML or PDF file. See 2D Viewer - Save Grid Image. In PDF format, the images are in the same grid layout as in the panel, with page breaks. In HTML format, the images are presented in a table in the same layout as in the grid. A file selector opens, in which you can choose the format and name the file.

  • Export Structures—save the structures to an SD file. A file selector opens, in which you can choose the format and name the file.There are two choices of the file content:

    • 2D SD—write the 2D structures to an SD file with the properties displayed in the panel. The default is not to include hydrogens in the 2D SD file.
    • 3D SD with SMILES—write the 3D structures to an SD file with a SMILES string for the structure stored as a property along with the properties displayed in the panel.
Settings menu

Change the display of the structures. The items on this menu are grouped by function and are listed below. A check mark is displayed next to items that turn on a feature to indicate that the feature is selected.

  • Grid Layout—Display all the structures in a grid of tiles. In the grid layout, you can rearrange the tiles by dragging them to a new location. This is purely for display: it has no effect on the order of the entries in the Project Table.

  • Single Structure—Display one structure at a time. When you choose this item, arrow buttons are shown above the display area, so you can step through the structures. You can also use the left and right arrow keys to step through the structures.

  • Columns—Choose the number of columns in the grid view from this submenu. This item is only available if you choose Grid Layout.

  • Link 2D Selection and Inclusion—When you select one or more structures in the 2D Viewer, automatically include these structures in the Workspace.

  • Display Entry Properties—Display selected entry properties in a list below the structure in each tile.

  • Manage Entry Properties—Select the entry properties that are displayed in each tile. Opens the 2D Viewer - Select Properties Dialog Box, where you can filter and select entry properties for display.

  • Highlight Aligned Substructures—Highlight the maximum common substructure (MCS) between the structure and the reference by coloring the bonds pink. For the reference, the MCS is a combinination of the MCS with all other structures.

  • Display Atom Annotation—Display the selected atom-level property for each atom instead of the atomic symbol. The property is displayed at the position of the atom and is displayed for all atoms, including carbon, and hydrogen if the Show all hydrogens preference is selected.

  • Choose Atom Property—Choose the atom-level property for the display of atom annotation. Opens a dialog box in which you can choose an atom-level property.

  • Show Neutral Form—Show the 2D structure in its neutral form, if it is ionic.

  • 2D Structure Preferences—Set preferences for 2D structures. Opens the Preferences Panel at the 2D Structure Preferences.

Display area

The structures are displayed in this area, in tiles arranged in a grid. If you choose Change view → Single Structure, only one tile is displayed.

The circle at the top left of a tile can be used to include the structure in the Workspace. This is equivalent to the button in the In column of the Project Table or Entry List. Inclusion of structures in the Workspace is synchronized between this panel and the Project Table and the Entry List: a change in one place changes the other two places. You can include multiple tiles with the usual shift-click and control-click actions.

Properties are displayed in a list below the structure, in a two-column layout with the name on the left and the value on the right. As the space is limited, the text may be truncated, but the full property information is displayed in a tooltip in the format name: value.

In grid layout, the tiles can be moved to a new location by dragging. This allows you to rearrange them as you want; it has no effect on the order of the entries in the Project Table.

You can select tiles with the usual shift-click and control-click actions. With a single tile selected, you can move the selection with the arrow buttons or with the N and P keys on the keyboard or the arrow keys. This is useful when you have Link 2D Selection and Inclusion selected, as the included entry changes as you move the selection. The selection of tiles is independent of the entry selection in the Project Table.

The display area has a shortcut menu for actions on the selected tiles, which is displayed on right-click. Right-clicking selects the tile if it is not already selected. The shortcut menu is grouped by function:

Workspace inclusion

These items control the inclusion and exclusion of structures from the Workspace based on the inclusion status of the structure in the tile you right-clicked. The action is taken on the selected structures. The inclusion items are only present if the clicked tile is not in the Workspace; the exclusion items are present if the tile is in the Workspace.

  • Include in 3D Workspace—add the structures to the Workspace, without changing the inclusion of other structures. Equivalent to control-clicking the inclusion buttons.
  • Exclude from 3D Workspace—remove the structures from the Workspace, without changing the inclusion of other structures. Equivalent to control-clicking the inclusion buttons.
  • Exclude Other Entries—remove all other structures from the Workspace, keeping these structure in the Workspace. Equivalent to including just these structures.
Project Table selection

These items control the selection and deselection of structures in the Project Table based on whether the structure in the tile you right-clicked is selected or not. The action is taken on the entries for the selected tiles. The inclusion items are only present if the entry for the tile clicked is not selected in the Project Table; the exclusion items are present if the entry for the tile is selected in the Project Table.

  • Select in Maestro Project—add the entries to the Project Table selection, without changing the selection of other entries.
  • Deselect in Maestro Project—remove these entries from the Project Table selection, without changing the selection of other entries.
  • Deselect Other Entries—remove all other entries from the Project Table selection, leaving these entries selected.
Tile actions

These items perform actions on either the tile you right-clicked or the selected tiles.

  • Copy This Image—copy the 2D image to the clipboard for the tile you right-clicked.
  • Set Structure as Reference—make the structure in the tile you right-clicked the reference structure. The 2D image of the reference structure is updated to match the orientation of the 3D structure in the Workspace, and is highlighted in light blue. If structures were aligned to a previous reference, the 2D image reverts to the default and is no longer highlighted.
  • Reset to Default Orientation—reset the orientation of the selected structures to their original orientation. Any alignment highlighting is removed.
  • Remove from 2D Viewer—remove the selected tiles from the 2D Viewer. This action is only available if Auto-update is not selected.
Previous and Next images

Drag cells to reorder. Display the previous or next structure with the P and N keys, or the left and right arrow keys. Right-click in the image for more options.

Reset button

Reset the panel to its default settings, clearing all data.

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