Diamond Version 5 User Manual: Working with Diamond

Picture Edit View and Thumbnails Preview

Multiple picture documents: Where to edit a structure picture and how to manage other pictures as thumbnails

The Diamond document window is split into two parts: A Pictures view in the left pane and a data pane in the right pane. This article introduces into the Pictures view and informs about options how to view and navigate to the structure pictures of a document:
- Editing a structure picture in the Picture Edit view.
- Pictures associated to a structure or all pictures of a document can be surveyed in thumbnails preview.
- Navigation tree for navigation through all documents.
- Caption bar for navigation (current document only).
- "More Pictures" docking window.
- Using tabs for preferred pictures or the pictures of interest when you have multiple pictures (of a structure data set).
- Expanding the Pictures view (and collapsing the data view).

Previous article: The Diamond User Interface
Next article: Side-by-side Structure Picture Editing

Picture Edit view

The regular case is to have your structure picture in the so-called Picture Edit view. That is where you have access to all functions to build up and design a picture, especially when you have selected one or more atoms or bonds or other objects to edit their properties or to use them as starting point for building up their coordination sphere or complete a molecule. That is also where you can rotate, shift, enlarge etc. a structure picture interactively with the mouse or cursor keys, for instance.

Screenshot of structure picture in Picture Edit view (in the left pane) with some atoms marked as selected and Atom Design dialog open. The right pane shows data sheet (upper right) and properties of the selected atoms (lower right).

Thumbnails Preview

The other case is to have a so-called Thumbnails Preview of all pictures in a Diamond document or at least of the pictures of the current structure.

While there are the "More Pictures" docking window and the "Picture Link Thumbnails" showing you other pictures than the one that is currently edited in the Picture Edit view - as described in this article below - only the Thumbnails Preview gives you a complete overview of the pictures in a document, including the option to copy or delete selected pictures.

Screenshot of Thumbnails preview (view type "Content") for sample file Na3PS4-10-pictures.diamdoc and "Super cell 2x2x2 ..." as preferred (tabbed) picture. The Pictures view has been expanded, data sheet and Properties view collapsed. See below "Expanding Pictures view".

As mentioned before, access to all picture building and designing function is only in the Picture Edit view, but some of the commands can also be applied to pictures when there are in thumbnails. This allows to target multiple picture at once with a single command. On the other hand, typical commands that are not available in Thumbnails Preview are functions that refer to individual atoms, bonds and other objects of a structure picture each.

The usage of the Thumbnails Preview is described in more detail in the article "Working with structure picture thumbnails".

Navigation tree

The Navigation window is a docking window, where the hierarchical structure of all currently open Diamond documents is displayed in a tree-like representation, the Navigation tree. It is a special kind of window that can be docked at different sides of the application main window; it may also float at top of the desktop.

Screenshot of Navigation window with picture "Super cell 2x2x2 ..." of Na3PS4-10-pictures.diamdoc as the currently edited (or selected) picture. Two additional documents are open: "1251073...diamdoc" and "cod-7106313...diamdoc".

The Navigation command to show (and put the input focus to) the Navigation tree can be executed either from the "View" menu or by pressing the keyboard shortcut Alt+N. If you would like to close the Navigation window, click on the "x" at its upper right corner.

The top level of the hierarchy (trunk of the tree) is represented by the name of the current Diamond document. A document may contain several crystal (or "molecular", i.e. without cell parameters and space group) structures, so these (crystal) structures form the next hierarchical level (the branches of the tree). For every (crystal) structure, there are associated views for one or even more structure pictures. These associated views form the uppermost hierarchical level (the leafs of the tree).

If you click on an element of the tree (trunk, branch or leaf), a corresponding view will be displayed in the main working area: If you click on the trunk (document name), a list of all crystal structures in the current document will be displayed in the upper half as well as a picture thumbnail overview of the complete document below along with the data sheet. If you click into a structure picture thumbnail, it will be enlarged to the full size, that means you will go to "structure picture edit view" (where you can change the properties of the picture, click on atoms, bonds, etc.)
If you click on a branch (crystal structure name), this is similar to marking a line in the list of all crystal structures: You will obtain a thumbnail overview over the corresponding structure pictures along with the data sheet. If you click into a structure picture thumbnail, it will be enlarged to the full size as described for the trunk. This is the same as the View -> Structure Overview command.
If you click on a leaf (structure picture), the corresponding structure picture view will be displayed in the main working area, that means you bring the corresponding picture into picture edit view.

If you would like to close the Navigation window, please click on the "x" at its upper right corner.

Caption bar

The Caption Bar comprises two functions in one bar: First indicating the current picture's title as well as the tile of the associated structure data set and the document it belongs to. Second it shows links to other pictures than the one currently in the Picture Edit view or the one selected in the Thumbnails Preview, rsp. Thus the Caption Bar offers a better orientation which structure data set and which document the currently edited picture belongs to as well as which additional pictures are available.

The left part of the Caption Bar shows titles of the current document, the current structure data set, and the current structure picture. The document and structure title use a link, that means you can click on the document link or the structure link to come to document overview or structure overview, rsp. This behaviour is similar to the above described Navigation tree - while the Navigation tree shows all open documents, the Caption Bar only for the current document.

The right part of the Caption Bar shows right aligned the other pictures that are available for the current structure data set. Every picture title contains a link you can click on to switch to the corresponding picture.

Screenshot of the Caption Bar (top). The Picture Tab Bar (below the Structure Info Bar) is also shown.

By default the Caption Bar is activated in Diamond version 5. To hide it temporarily use the Hide command from the Caption Bar sub-menu of the View menu. "Temporarily" means that the caption bar will be back the next time you run Diamond or when you close a document and open another document in Diamond. If you dislike the caption bar, you can hide it with the command Hide Permanently. Anyway, the Show command can be used to re-activate the caption bar manually.

Note: The tab bar (preferred pictures) and link bar (the rest of the pictures), which were introduced in version 4, can be used additionally or alternatively to the caption bar, see "Using tabs" below.

More Pictures docking window

The More Pictures docking window shows thumbnail pictures of all pictures of the document (or of the current structure only) or all but the current picture. As a docking window (which can also be floating) this overview of pictures beside the one that you are editing in the main Picture Edit view is more flexible than the picture link thumbnails that were introduced with version 4. The default position is the left side of the Diamond application window, but you can also dock it on the right side.

The More Pictures window complements the Navigation tree as well as the picture tabs and link thumbnails, which are still available, see "Using tabs" below.

Note: A docking window containing all structure picture thumbnails was already available in version 3 with the title "Thumbnails", but was abandoned in version 4 in favour of the picture tab bar and picture link thumbnails. The name "Thumbnails" is used for the "Thumbnails Preview" instead since version 4.

The context menu of the More Pictures window offers options to
- either show pictures of the current structure only (if there may be multiple structure data sets defined in your document/file): Show Pictures of Current Structure Only,
- or to show pictures of the whole document/file: Show Pictures Of All Structures.
Besides this, you can decide, if to show the picture in the Picture Edit view or not (since it is actually not necessary to show it twice): Hide Thumbnail of Current Picture.

Screenshot of the "More Pictures" docking window with context menu showing that only pictures of the current structure data set are regarded and the currently edited structure picture is shown redudantly in the "More Pictures" window.

You can activate the More Pictures docking window with the corresponding command in the View menu or directly from the toolbar button or with the acceleration key Alt+I:

Using tabs

Editing a structure picture while glancing at the others
May be you just edit one single structure picture in your Diamond document, but when you create different views of your structure, may be with various designs for printing or for a presentation, it is practically to have thumbnails of at least some of the other pictures at a glance.
Some of them may be more important than the rest - for the moment you are editing. So you can arrange your preferred pictures on tabs, while you have access to the residual pictures by link buttons. (This may remind you - not coincidentally - at tabs in Internet browsers.)

A preferred picture under a tab
The default or regular case is a "preferred" picture under a tab, whereas the residual N-1 pictures appear either as links or as thumbnails below the picture in the Picture Edit view. (If there is just one picture, there is one tab in the tab bar and the link bar is empty.)

Switching to other pictures
You can edit another picture by clicking on the link button, bringing the clicked picture into the same tab. Or you can open the clicked picture in another tab. This may result into multiple tabs, if you have multiple "preferred" pictures.

Show tab thumbnails
One of the "preferred" pictures is under the "active" tab in the Picture Edit view and the thumbnails of the residual preferred pictures are right beneath the Picture Edit view.

Switching tabs and links on or off
The Diamond version 4 style tab bar and link bar (or the tab thumbnails or link thumbnails) can be switched on or off from the sub-menu View/Pictures Viewing. The easiest way is to use the command Tab and Link Overview. Tabs and links can be switched on or off individually using the commands Show Tab Bar etc. in the mentioned sub-menu.

The usage of the tab bar for the "preferred" pictures and the link bar for the "other" pictures is described in detail in the following article: Side-by-side Structure Picture Editing.

Expanding the Pictures view

You can (temporarily) expand the pictures view (which either hosts the Picture Edit view or the Thumbnails Preview) to almost the full width of the document window. by collapsing the data sheet or data table shown in the right pane.

The command Expand Pictures View, which expands the structure picture view and collapses the data sheet (or table) or restores from expanded pictures view, is available from the View main menu in the Pictures Viewing sub-menu. The corresponding icon >> is available from the main toolbar - and also from the picture tab bar, unless this bar is hidden (which is the default setting in version 5):

Previous article: The Diamond User Interface
Next article: Side-by-side Structure Picture Editing