|
|
2D Viewer Panel |
The 2D viewer allows you to display 2D structures for entries in the Project Table, in a rectangular grid, and use them to select and include structures.
To open the 2D Viewer panel, you can:
Choose Project → 2D Viewer in the main window.
Choose Table → 2D Viewer in the Project Table panel.
Click the 2D Viewer button on the Project toolbar in the Project Table panel.
Click the 2D Viewer button on the Project toolbar in the main window.
The basic function of the 2D Viewer panel is to display 2D representations of the structures in the Project Table and provide capabilities for selecting and including the entries from this panel.
The 2D structures are images that are created when the panel is opened, or when you click Update 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 images can be exported in various formats.
In addition to the structures, properties can be displayed below the structures in each cell. Real properties are displayed to the same precision as in the Project Table. You can also display an atom-level property, such as the atom name, instead of the atomic symbol. To select properties to display, choose Edit → Select Properties.
Each cell in the display area corresponds to an entry in the Project Table. You can select cells with the usual shift-click and control-click actions, and you can drag to select cells.With a single cell selected, you can step through the structures with the arrow buttons or with the N and P keys on the keyboard.
The selection is independent of the selection in the Project Table by default, but you can make the panel selection and the Project Table selection the same by selecting Synchronize selection with Project Table.
The inclusion state is always the same as in the Project Table, and is indicated by the square in the top left of each cell. You can automatically include in the Workspace the structures that you select in the panel by selecting Include selection in Workspace. With this option, whenever you select a table cell, the structure is included in the Workspace.
This menu allows you to edit the display settings and the list of properties that is shown for each entry.
Copy—Copy the image for the selected cell to the clipboard, where it can be pasted into another application. You can also use Ctrl+C (⌘C) to copy the image. Only one cell must be selected.
Select Properties—Choose the structure properties to display in each table cell in the display area. Opens the 2D Viewer - Select Properties dialog box, in which you can select the properties to display.
Settings—Set options for the export of structures. Opens the 2D Viewer - Settings dialog box to make the settings.
2D Display Settings—Set options for the display of the 2D structures. Opens the Preferences panel at the 2D structure group.
This menu allows you to export selected 2D structures in a variety of formats.
Export to PDF—Export the structures as images in a PDF file, in an array with the same number of columns as in the panel. Opens a dialog box in which you can navigate to a location and name the file. The properties displayed with the structure are included in the images. Images are exported as scalable vector graphics.
Export to PNG—Export the selected
structures to separate PNG files. Opens a dialog box
in which you can navigate to a location and provide a base name for the files.
The files are named base-NNN.png, where
NNN is a serial number for the image, starting from 001. Only the 2D
structure is included in the image.
Export to HTML—Export the selected
structures as PNG images included in a table in an HTML page, with the same
number of columns as in the panel. Opens a dialog box
in which you can navigate to a location and name the file. The images are
exported into a directory in the same location. If the file is named
myimages.html, the image directory is named
myimages_img and the image files are named
myimagesN.png, where N is an index starting from 1.
The links to the images are relative, so the file and image directory can be
moved to another location easily. The structure title is included as alt text
for the image. The properties displayed with the structure are included below
the image in the HTML file.
Export to 3D SD with SMILES—Export the selected structures to an SD file as 3D structures (not 2D structures), with the unique SMILES string added as a property.
Export to 2D SD—Export the selected structures as 2D structures to an SD file.
Export to EPS—Export the selected
structures to separate encapsulated PostScript files. Opens a dialog box
in which you can navigate to a location and provide a base name for the files.
The files are named base-NNN.eps, where
NNN is a serial number for the image, starting from 001. Only the 2D
structure is included in the image.
This menu provides choices for selecting structures in the 2D viewer.
The Previous and Next items only work if there is only one structure selected. They perform the same task as the navigation buttons.
Choose the number of columns to display in the viewing area, from 1 through 10.
This option menu allows you to choose which entries to display in the 2D viewer:
Update the structures that are displayed in the 2D viewer with the entries in the Project Table according to the choice made from the option menu. The display is not updated automatically when the Project Table selection, inclusion, or content is changed. This button allows you to refresh the display to reflect the latest inclusion, selection, or content.
These options allow you to choose whether to display all the structures in a grid, or only the selected structure. You can also press ENTER to switch between grid and single entry display.
Use these buttons to move the selection to the next or the previous structure. These buttons are only active if you have a single structure selected in the display area. (When zoomed in, the displayed structure is the selected structure, even though its background is no longer colored.) You can also change the selection with the arrow keys.
Change the selection in the Project Table to match the selection in the 2D display area.
Include the structures that are selected in the display area in the Workspace. The content of the Workspace changes as the selection in the 2D display changes, and the inclusion state in the Project table also changes.
Display the 2D structures in a table, with the number of columns that was chosen from the Columns menu. Multiple structures can be selected by dragging or with shift-click and control-click. The square in the upper left corner of each cell displays the Workspace inclusion state, and can be used to include or exclude entries from the Workspace, just as for the In column in the Project Table.
Clears the 2D viewer.
|