Diamond Version 5 User Manual: Working with Diamond

The Diamond User Interface

Structure picture, tables, distances, powder pattern, etc. side-by-side

This article in brief:
- Start Page
- Document window
- Caption bar
- Structure info bar or table of structure data sets
- Structure picture pane (Picture Edit view and Thumbnails Preview)
- Data sheet, tables of atoms, bonds, etc., atom list
- Properties view
- Distances and angles, powder pattern
- Docking windows: Navigation, More Pictures, Recent Pictures, Undo Buffer, Auto Picture Creator

Previous article: About documents, structures, and pictures
Next article: Picture Edit View and Thumbnails Preview

Start Page

When you start the Diamond application, it comes up with the so-called "Start" page, presenting a list of recently opened or saved files ("most recently used files") and a list of recently used structure pictures as well as links to help files and to the Crystal Impact web server. You can easily select the most common operations, e.g. open a structure data file or create a new document, or access one of the most recently used files or pictures. Besides this, you can access infos, the online help, and the Diamond-related web pages of the Crystal Impact web site. Latest news, typically news about new versions/patches of Diamond, are given in the rightmost column.

Opening or importing from structure files as well as accessing latest used files or latest edited/viewed pictures is described in the articles "Opening and importing structure files" and "Recent pictures".

You can change the maximum number of files in the list of "most recently used files" on the Desktop page of the Options dialog, available from the Tools -> Options command. This also affects the number of "most recently used files" listed at the bottom of the File menu.

By default, the "Start" page is shown automatically whenever you start Diamond. To switch off this option, run the command Tools -> Options and change to the Desktop page (tab) of the Options dialog. In the When Diamond application is started group clear the radio button at Show Start page.

If you do not make use of the automatic display of the "Start" window, it can also be displayed anytime later while Diamond is running, simply by selecting the Start Page command from the Help menu.

The "Start" page also closes by default when you open a recent file or recent picture. To keep the "Start" page open, clear the checkmark at Close Start page after opening ... in the Options dialog. Please note that the "Start" window will be hidden (but not closed) when a new document window is opened for the recent file/picture you are accessing. The "Start" window is then available through the Window menu. In any case you can switch back to or re-create (if closed) the "Start" page with the command Start Page in the Help menu.

Document window

The structure pictures view is the most important element of the Diamond application screen allowing you full access to all picture building and designing functions and to manage pictures (copy, delete), if there are multiple pictures in the document. The structure picture view is assisted by several textual views in the right data pane: tables (e.g. of atomic parameters), data sheet, but also table of distances and/or angles or table of reflection parameters.

The screenshot below shows (on the left) the More pictures docking window, (on top) the structure table, (bottom centered) the structure picture edit view, (right centered) the data sheet, and (bottom right) the properties view. For the screenshot, the sample file PCD-VxOy.diamdoc has been opened and the structure data set "PCD:455496" focused. (Click here for a bigger image):

The views and panes are:

(A) Caption bar showing the title of the active picture (here: "Picture1"), the title of the current structure data set (here: "455496"), and the title of the document (here: "PCD-VxOy.diamdoc").

(B) Structure table showing all structure data sets of the document with the active structure marked.

(C) Structure picture (here: "Picture 1" of data set "455496") in "Picture Edit view" with title tab at the top and links to other structures' pictures at the bottom. (To show tab and link buttons, use the command View -> Pictures Viewing -> Show Tab and Link Bar. Find details about tabs, links etc. in a separate article "Side-by-side Structure Picture Editing".)

(D) Data sheet (here of data set "455496"). The data sheet is configurable as "comprehensive" and "brief" (which is the default setting and used here).

(E) Properties view - here with the default setting: the properties of the current structure picture.

(F) Docking panes, here with "More Pictures" window in the foreground and "Recent pictures" and "Navigation" in the background. [Show Pictures of All Structures] (To open "Recent picture" or "Navigation" click on the tabs at the bottom of the docking windows, if available, or use the corresponding commands from the View menu.)

Caption bar

The Caption bar shows the name of the active document, the title of the active structure data set, and the title of the active structure picture. Besides it shows titles of additional pictures that are defined for the current structure data set. (Note: The Caption bar shows only pictures belonging to the current structure.)

The Caption bar is described in more detail in the article "Picture Edit View and Thumbnails Preview".

To show or hide the Caption bar use the commands from the View -> Caption bar sub-menu.

Structure info bar or table of structure data sets

You will find the structure table (for a document with more than only one structure parameter set) in a pane above the structure picture and data panes. The structure table can collapse to save space to show only a compact info in one row for the current structure, that is called the "structure info bar". The structure table will be described in more details in the articles "Working With Structure Picture Thumbnails" and "Color coding of structural parameter sets".

To switch between info bar and table or to choose the columns to be displayed, choose the commands in the View -> Structures sub-menu.

Screenshot of the structure table from the sample file as above

Short screenshot of the same sample file as above - but with structure table collapsed as info bar. (Tabs for pictures are below the structure info bar, see: Side-by-side Structure Picture Editing)

Structure picture pane: Picture Edit view and Thumbnails Preview

The left and main pane of the document window hosts the structure picture you are editing or an overview of the structure pictures as thumbnails (if you have multiple pictures in your document). There are two different views: The Picture Edit view to edit a single structure picture (or one of multiple pictures) - and the Thumbnails Preview where you can manage the pictures (e.g. copy or delete pictures) but only have limited access to the full functionality of Diamond's picture building and designing capabilities.

Picture Edit view and Thumbnails Preview are described in the next article: Picture Edit View and Thumbnails Preview.

Data sheet, tables of atoms, bonds, etc., atom list

The data pane or "secondary pane" is the pane right beneath the pane hosting the structure picture you are editing or the structure picture thumbnails you are organizing consists of two parts, an upper part with the data sheet or several kinds of data tables and a lower part that hosts the Properties view. Find details about the data pane in the article "Data Pane: Data sheet, tables, properties view, and atom list".

The upper part of the data pane offers several tables for created atoms, bonds, and molecules (or fragments) as well as for atomic, bond, H-bond, and contact parameters. There are also special tables for objects like polyhedra or planes.

The article "Tables of objects like atoms, bonds, molecules etc." describes how to work with these tables, especially to select objects in the structure picture or - vice versa - to find informations about an object in the table hat has been clicked (selected) in the structure picture.

Another, special kind of table is the Atom list, which either shows the created atoms grouped for atom sites and atom groups, or arranged by molecules. You will find details about the atom list in the article "Atom list: Hierarchical list of atom groups, atom sites, and created atoms of a structure picture".

Screenshot of sample file COD-1500005-molecules.diamdoc: On the left side: table of created molecules, on the right side: the atom list

Properties view

The Properties view shows informations in context with the current situation, e.g. the contents of the structure picture you are working with, properties of the selected atom, distances around the selected atom, centroid or best plane or line through selected atoms, and many more.

The screen shot below shows an info about the currently selected object. The atom "V(1)" is selected in the table of created atoms (and in the structure picture), the "Object info" is given in the Properties view.

The Properties view gives you information of the following kinds:

• Contents of the structure picture (how many created atoms, bonds, polyhedra, etc.).
• The current "formula sum", that means the number of created atoms associated to atom groups.
• Info about the object that is selected in the structure picture or in the (optional) table above the properties pane, e.g. info about an atom of the parameter list.
• Table of the currently selected objects.
• Distances around the selected atom(s).
• Distances between the selected atoms.
• The center of the selected atoms (centroid).
• The planarity or linearity of the selected atoms and the deviations of the atoms from that plane or line, rsp. (See also feature "Geometric enhancements".)
• Table of atoms assigned to the selected atom of parameter list or selected atom group.
• Table of bonds assigned to the selected bond group (i.e. atom group pair).
• Ligand, edges, and faces informations of the selected polyhedra.
• Dirichlet domain of a selected atom site.
• Neighbouring atoms and vertices of a selected Voronoi polyhedron.

Find more details about the properties view in the article "Data Pane: Data sheet, tables, properties view, and atom list".

Distances and angles, powder pattern

The data pane also hosts the Distances and angles view, with the table of distances and/or angles in the upper part and a distances histogram in the lower part (in the Properties pane), as well as the Powder pattern view, with the reflection parameter table and the diffraction diagram below:

Screenshot of sample PCD-VxOy.cif with "455496" focused: Distances table and histogram in the left part, and powder pattern in the right part

The advantage of having distances and angles view as well as powder pattern view right beneath the structure picture view rather than in a separate view is to correlate the distances with the atoms in the structure picture. For instance, the table of distances can automatically follow the currently selected atom(s) as centers for its distance calculations.

The use of the Distances and angles and Powder pattern views are described in details in the articles "Table of distances and angles" and "Powder pattern simulation", rsp.

Docking windows: Navigation, More Pictures, Recent Pictures, Undo Buffer, Auto Picture Creator

Screenshot of docking windows for recently used pictures, navigation tree for all opened files, and pictures belonging to the current open document

A "docking window" is a special kind of window (not to be mismatched with a "document window", where you edit or manage structure pictures, and which is associated with a file) that can be docked at different sides of the application main window. It may also float at top of the desktop.

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.

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, giving you an overview of pictures beside the one that you are editing in the main Picture Edit view (or which is marked as selected in the Thumbnails Preview).

The "Navigation tree" and the "More Pictures" window are described in details in the article "Picture Edit View and Thumbnails Preview".

The Recent Pictures window lists thumbnails of the recently used (edited) structure pictures in descending order of the last access and is described in the article "Recent pictures".

In the Undo Buffer window thumbnails of the picture's conditions before the command execution each are presented, with the latest action on top. A tooltip window may offer you additional information, for instance how many atoms or bonds were created in the latest step of a building command. This docking window is described in the article "Undo buffer".

The Auto Picture Creator docking window offers the most useful features to create a structure picture automatically or by scheme. It automatically applies changes in building options, picture design, and viewing direction directly to the structure picture. The "Auto Picture Creator" is described in the article "Auto Picture Creator".

Previous article: About documents, structures, and pictures
Next article: Picture Edit View and Thumbnails Preview

References:
PCD:455496: VO2(B) in C12/m1 (12). Oka Y., Yao T., Yamamoto N., Ueda Y., Hayashi A.: Phase Transition and V4+-V4+ Pairing in VO2(B). Journal of Solid State Chemistry, 105, 271-278 (1993).
COD:1500005: Hexaammine cobalt(III) hydrogenarseniate tetrahydrate; Ritu Bala, Raj Pal Sharma, Rajni Sharma, Juan M. Salas, Miguel Quiroos, William T.A. Harrison: Cationic cobaltammines as anion receptors: Synthesis, characterization an X-ray structure of bis-(hexaamminecobalt(III)) tris-(hydrogenarsenate) tetrahydrate; Journal of Molecular Structure, 828, 174-180 (2007).