Diamond Version 5 User Manual

This article serves as the table of contents of the user manual and offers a series of HTML articles covering several aspects of how to work with Diamond.

Main topics

Working with Diamond

Structure files

Editing structural data

Automatic, assisted, and manual picture creation

Modes of operation

Exploring bonding and contact spheres

Building up structural parts

Display of structure picture

Polyhedra

Distances and angles

Data sheet and powder pattern

Printing, copying, and exporting structure pictures

Working with Diamond

About documents, structures, and pictures
A Diamond document may contain multiple structural parameter sets and multiple pictures for every structure.
- About crystal and molecular structures
- One or more pictures for a structure parameter set each
- Multiple structure parameter sets
- Multiple documents
- Exchanging data between documents

The Diamond User Interface
Structure picture, tables, distances, powder pattern, etc. side-by-side.
- 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

Picture Edit View and Thumbnails Preview
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).

Side-by-side Structure Picture Editing
You can view structure pictures (if a document contains multiple structure pictures) side-by-side:
- A preferred picture under a tab, whereas the residual N-1 pictures appear either as links or as thumbnails below the picture in the edit view.
- Multiple tabs.
- Edit another picture by clicking on the link button in the same tab, or in another tab.
- Edit view and thumbnails of the residual preferred pictures right beneath the edit view.

Working with structure picture thumbnails
The structure picture thumbnail view offers:
- Settings Tiles, Content, and Details.
- Grouping of pictures by structure data sets (multiple pictures for multiple structures in a document).
- Sorting options.

Color coding of structural parameter sets
- Colored rows in structure table. Colored group headers in data sheet.
- Colored tabs of preferred structure pictures as well as link buttons.
- Colored frames around picture thumbnails.

Data Pane: Data sheet, tables, properties view, and atom list
The data pane in the right half of the document window offers several auxiliary views to work with structure pictures:
- Data sheet or tables of atoms, bonds or other objects or atom list in the upper part and properties view in the lower part.
- Data sheet: overview of contents, different configurations.
- Table of atomic or connection parameters or table of created atoms, bonds, or other objects.
- Properties view: showing infos about the selected atom, bond etc. (in picture or in table).
- Atom list: a hierarchical list of atom groups, atom sites, and created atoms of a structure picture - or a list of molecules and their constituent atoms.

Recent pictures
Access the latest viewed and/or edited structure pictures.
- Applies to pictures from current as well as earlier Diamond sessions.
- "Recent pictures" docking window: contains latest edited structure pictures of open document as well as of recently closed documents (files).
- "View/Last pictures": Access to latest edited pictures of current open document (also available from toolbar).
- Direct access (toolbar button) to latest edited picture, so you can swap between two pictures of interest.
- Clear Recent Pictures Buffer command to delete all recent picture informations.

Undo buffer
-  Undo/Redo can be done with multiple steps together, assisted by thumbnail pictures of the previous conditions.
- "Undo/Redo" docking window: Click on a thumbnail to restore all undo steps through the clicked one. The same works for redo steps, if undo steps have been performed immediately before. Slight differences in shape between the two kind of undo and redo thumbnails.
- Dropdown list from toolbar with thumbnail of last undo and redo, rsp., steps.

Full screen view of structure picture
- Toolbars, docking windows, status bar and menu bar are hidden, and the document window occupies the full screen.
- Options to temporarily also hide data pane etc. and to have the structure picture being the only view in full screen mode will come in a later version.

Importing Registry settings and recent pictures
- Using the Start page to import settings or recent pictures
- Import of settings
- Export and reset of settings
- Import of recent pictures (command in Recent Pictures docking window)

Structure files

File formats
- Diamond Version 3,4,5 Document Format (diamdoc)
- Diamond Structure File Format (DSF 2)
- Endeavour File formats
- Foreign File Formats
- Compatibility with Diamond 1.x File Format

Opening and importing structure files
- Opening structure files
- Multiple structure descriptions in one file
- Importing data from a file
- Loading another structure from a file
- File Import Assistant
- Opening a recently used picture

Inserting structure data into a document
About several ways to add one or more structure data sets into a new blank document or to add another structure data set(s) into an existing document.
- "Structure/Insert From File" enables you to add one or more structure data sets from one or more files.
- "Structure/From Structure Type Database" lets you add structure data from an inorganic structure type database.
- With "Structure/New Structure" you can add structural parameters manually or from a structure template to an existing document.

Access to COD ("Crystallography Open Database")
- This crystal structure database includes (amongst others) AMCSD ("American Mineralogist Crystal Structure Database") as well as CIF files from the IUCr journals.
- How to setup the COD for Diamond version 5 -- not more available through installation package.
- How to search the database through "File/Search..." command.

Searching of files
Search Diamond documents and structure files on your hard disk
- File, folder, and format selection.
- Defining restraints for chemical composition, crystallography, as well as bibliographic references.
- Search for text strings and fragments in files.

Database with inorganic structure types
Diamond comes with a small database with the most common inorganic structure types. You can use the command "From Structure Type Database..." in the "Structure" menu to browse through a list of structure types and insert a dataset from this database into the current document.
The "Structure/Insert From Structure Type Database" command/dialog has an option "Load structure picture(s)", which enables you to load one or more ready-to-use structure pictures for the selected structure type.
Besides this, the "New Document" dialog (via "File/New..." command) has an option (radio button) "Load a structure from structure type database", which forwards you to the command "Insert From Structure Type Database..." ("Structure" menu).

Saving and exporting structure data
- Saving Structural Data
- Saving Structure Data in Foreign Formats
- "Save Structure As" command
- "Export" command
- Auto Save function
- Temporary files

Editing structural data

Entering a new structure
- Creating a new document
- Creating a new structure
- Using the "New Structure Assistant" to enter structure parameters and options for the first structure picture
- Adding another structure to a document
- Separating a structure

Bibliographic data
- About data fields used as bibliographic data
- How to edit bibliographic data.

Symmetry and cell parameters
- Space group
- Cell parameters
- Structures with no cell and symmetry ("molecular structures")
- Converting molecular structures into crystal structures and vice versa.

Atomic parameters
- Atomic parameters dialog with report-like representation of atoms and grouping of sites.
- Editing of atom's properties can be performed directly in the row of the table of atomic parameters.
- Multiple atom parameters on one and the same site each, i.e. the mixed sites' components, are displayed under a tree branch.
- Symmetry equivalent positions (as come often from CSD-imported CIF files, in order to describe complete molecules when the asymmetric unit only reflects a fraction of those molecules) are marked separately.
- Edit (and doing copy/paste) properties of multiple atoms at a time.
- Table of atomic parameters.

Connection parameters
These parameters are usually imported from "_geom_bond_xxx", "_geom_contact_xxx", and "_geom_hbond_xxx" loops in CIF
- Parameters are editable in the dialog "Structure/Connection Parameters", which has three tabs (pages).
- Tables of bond, H-bond, and contact parameters are available from the "Tables" sub-menu of the "View" menu.

Automatic, assisted, and manual picture creation

Automatic vs. manual picture creation
This article and the following articles are about the difference between automatic picture creation and the several ways to build up a structure picture manually step by step.
- Options if and how to create a picture automatically (proposal or by scheme or from Auto Picture Creator settings).
- Status of what happens when picture start now shown and changeable in status bar.
- Improvements in structure picture proposals.
- Applications of building and design schemes.

Picture Creation Assistant
An optional assistant helps you to create a (new) structure picture.
- Starting from scratch or modifying an existing picture.
- Basic building functions.
- Adding additional atoms, bonds, or polyhedra.
- Creating a packing diagram.
- Defining the picture design.
- Choosing viewing direction and projection.
- Defining additional objects.

Auto Picture Creator
This is a docking pane offering the most useful features in the categories picture building, picture design and picture viewing at a glance.
- Picture building category contains settings for a building scheme, including packing diagram as well as contact and H-bond options.
- Automatically (optionally) applies changes in building options, picture design and viewing direction directly to the structure picture.
- (User-defined) building schemes and/or design schemes can be used.

Building schemes
A "building scheme" is a set or batch of commands to build up a structure picture.
- Several commands available through "Build/Building Scheme" sub-menu.
- "Define Scheme" to define a new scheme or by modification of an existing scheme.
- "Run Proposed Scheme" to run the building scheme that Diamond suggests basing upon structure data.
- Apply Building Scheme from a list in the sub-menu or from the "Run Building Scheme..." dialog.

Definition and application of "design schemes" (style sheets)
- Available from the "Display/Design Scheme" sub-menu.
- Creation: Use current picture design and viewing settings and save these in a (new) design scheme: "Create Design Scheme From Picture...". Or use designs of the currently selected atoms, bonds (contact, H-bonds), and polyhedra in a design scheme using "Create Design Scheme From Selection...".
- "Apply {Design Scheme Title}": Apply previously defined design schemes directly to current picture or selection.
- "Apply Design Scheme": Choose a design scheme from the dropdown combobox list and apply it -- either directly or after some modifications.
- "Design Scheme Manager" (Display sub-menu or Tools menu).

Optimizing the Representation of the Structure Picture
- Different targets to optimize your structure picture for.
- Using the Picture Creation Assistant to change or optimize an existing structure picture.
- Using the Auto Picture Creator docking window.

Deriving new pictures
Use "Take picture" and "Continue with new picture" to improve your work flow of creating pictures.
- "New Blank Picture" to create a new blank picture object and start building from scratch.
- "Copy To New Picture" to create a copy of the selected parts of the active structure picture.
- Using the Picture Creation Assistant to define what happens with the target picture.
- Creating new pictures from the tab bar.
- "Take picture" and "Continue with new picture" create a new structure picture object as a complete copy of the current picture.

Modes of operation

Overview
This article is an overview about the different operational modes when working with a structure picture:
- The default mode: Select and Edit
- Tracking modes: Mouse-controlled rotation, shift, and enlarging of structure picture
- Grab mode
- Exploration view
- Measuring modes (distances, angles, etc.)
- Command-specific operational modes

Selecting objects
- How to select objects of the structure picture (atoms, labels, etc.).
- Normal vs. additive and subtractive selection. Usage of Ctrl and Shift key.
- Selecting the molecule when you click an atom, or expand selection to whole molecule.
- Expanding or reducing selection stepwise to/from the next (bonded) neighbouring atoms and bonds.
- Using the mouse wheel to expand current selection to neighbouring atoms and/or bonds.
- Selecting disorder parts.
- The "Selection Filter" enables you to choose object types (atoms, bonds, labels, etc.) that are to be considered when you click on objects in the structure picture. This reduces inadvertent matching of wrong objects.
- Selecting fragments, i.e. any moiety of atoms with connecting bonds.
- Selecting other objects than atoms and bond, e.g. labels of selected atoms.
- Selecting atoms and other objects at symmetry-related positions.

Tables of objects like atoms, bonds, molecules etc.
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.
- Overview of tables and their contents and settings
- Selecting Atoms, Bonds, or Polyhedra From an Object List
- "Select in table" command
- Selecting atoms, bonds, or contacts from tables.

Atom list
The "atom list" is a hierarchical list of atom groups, atom sites, and created atoms of a structure picture -- or a list of molecules and their constituent atoms.
- Used for instance to edit properties and designs or to select from.
- Two kinds of arrangements: 1) For atom groups, sites and created atoms. 2) For molecules and their constituent atoms.
- Settings, if and how to group items.
- Plus/minus signs (and commands) to collapse or expand trees of items.
- Preview of atom design in first column.

Grab mode
The "grab mode" is an alternative to the several "tracking modes" with the advantage to be able to rotate, shift, or zoom in/out without the need to change between the several tracking modes. Features of grab mode are:
- Rotation with left mouse button.
- Shifting with right mouse button.
- Changing enlargement factor or camera distance with mouse wheel.
- Several options available with mouse button double click.

Neighbouring preview of atoms and molecules around the atom (molecule) under mouse cursor
- Move mouse cursor over an atom and see its neighbouring atoms (and molecules, if molecular structure) as semi-transparent preview.
- Turn mouse wheel forward/backward to increase/decrease the preview sphere size.
- Neighbourhood preview can also be applied to whole molecule.

Exploring bonding and contact spheres

Overview
- How and when to use Exploration View
- Activating this view mode
- Start Exploration dialog
- Graphics view and exploration controller
- Starting from a blank picture or from an already built picture
- Using the current picture or a copy for the exploration
- What to explore in this mode

Working in Exploration View
- The Exploration Controller
- Creating a single atom or molecule or cell content
- Rotating, shifting, and scaling your picture
- Growing or shrinking spheres around atoms
- Completing molecular fragments or cutting back molecules
- Taking or copying an image of the picture
- Closing Exploration view

Exploring bonding spheres
- About bonding spheres, connectivity, and atomic environments
- Starting from a single atom of the parameter list
- Using "Get Molecule" or "Fill Unit Cell"
- Example COD:7106313
- Example antimony trifluoride/pentafluoride adduct (Sb4F16)

Exploring H-bonds and contact spheres
- About H-bonds and contact spheres and how they are defined (connectivity)
- Example: H-bonds in a spirocyclic keto-lactam (COD:7106313)

Using Exploration view with an individidually designed structure picture
How to explore bonding or contact spheres in an already prepared structure picture
- About saving and restoring individual atom and bond designs
- How to make restored design undone after return from Exploration view by using the Undo command.

Building up structural parts

About atoms, atom groups, bonds, and bond groups
- Definitions
- About mixed sites and about atom groups
- Assigning a New Atom Type at Runtime
- About atom codes, bond groups, created atoms, and created bonds

Filter
- Exclude unwanted atom positions or symmetry operations from being used in most of the building operations
- Effects of the Filter

Connectivity, part 1: Bonding spheres
- About connectivity and which atom groups are connected and the sizes of their bonding spheres.
- Bond parameters are considered to extend the bonding spheres from mean bond lengths and effective radii.
- Connectivity dialog now has variable width and height.
- Indicators for changed/updated bonding sphere boundaries in the table of atom group pairs.
- Distances from bond parameters appear as ticks in the distances histogram.

"Atomic environment" as additional (optional) criterion when filling a coordination sphere or adding coordination polyhedra
- Definition of atomic environments for an asymmetric atom site each enables more precise definition of neighbouring atoms connected with strong bonds than just the connectivity which is defined between atom groups and by rather simple two sphere boundary values rmin and rmax each.
- Dialog "Build/Atomic Environments" to edit (add or remove) atoms from the central atom's environment each. Two presentations: Distances table and histogram.
- Correlation (optional, by default: yes) between atomic environments and connectivity (bonding spheres from atom group pairs).

Determination of atom site environments basing upon Dirichlet domains (Voronoi polyhedra)
Atomic environment can be derived from the Dirichlet domain (Voronoi polyhedron) of the central atom site each.

Support for disorder parts
- Functions that connect atoms and search for neighbouring atoms or complete molecules consider, if and what disorder part the atoms belong to and avoid connections between atoms of different parts.
- The "Filter" dialog offers a list of disorder parts making it easier to disable atoms from unwanted disorder parts to be considered in building operations like "Fille unit cell" or "Create molecules".
- The command "Select Disorder Part" ("Edit" menu) selects all atoms (and bonds between) belonging to the same disorder part as the selected atom. This is useful to edit atom and bond designs of disorder parts to differentiate them from other parts.
- Disorder information can easily be edited in the "Atomic Parameters" dialog and is shown in the info tip (mouse over atom) as well as in several dialogs (tables to select atom sites from) and as additional columns in table of created atoms and table of created bonds.  

Adding some or all atoms (and bonds) directly
- Adding some atoms from parameter list
- Adding all atoms (and bonds) of the parameter list(s)
- Adding atoms directly from the atomic parameter list

Filling cell ranges
- Filling the Unit Cell
- Filling a Super Cell
- Filling a Cell Range
- Filling Boxes or Spheres Around Selected Atoms
- Filling a Rectangular or Circular Area of the Screen

Cell edges
- Adding Cell Edges
- Designing Cell Edges
- Removing Cell Edges

Generating bonds directly
- Connecting all or selected atoms
- Consideration of individual atom sites possible in "Connect Atoms" dialog.
- Inserting a bond between two atoms
- Creating bonds directly from the Table of bond parameters

Filling spheres
- Fixed vs. Generic Spheres
- Filling Fixed Spheres
- Filling Coordination Spheres Around Selected Atom Groups
- Filling Coordination Spheres Around Selected Atoms
- Filling Coordination Spheres in Multiple Cycles
- Features of the "Coordination Spheres" dialog

Creating and modifying broken-off bonds
- Creating Broken-off Bonds
- Using Broken-off Bonds dialog to convert or delete broken-off bonds
- Using atom style "invisible" to simulate broken-off bonds

Generating molecules
- Define molecular units from the atomic parameter list basing upon connectivity or atomic environments.
- How the Molecular Generator Works
- Molecule Cage: Special Settings for the Molecular Generator
- Generating molecules from atomic parameter list

Completing molecular fragments
- Completing all or selected molecular fragments directly
- Complete Fragments dialog applying to atoms of selected atom groups or selected sites.
- Manual creation of packing diagrams.

Adding and finding symmetry-equivalent molecules
- "Build/Molecules/Add Molecules" to create molecules at symmetry-equivalent positions (by applying symmetry operations, and/or Bravais translations and/or integer cell translations) to molecular units.
- "Build/Molecules/Find Molecules" to search for molecules around selected atoms or molecules in order to create, complete, or destroy them.

Packing
There are several options to create (cell range, sphere, slab, or slice of molecules) and how far to include molecules:
- Comprehensive two-pages dialog "Build/Packing...".
- Page "Choose Atoms" to choose the molecules to be considered, how to treat polymers, and if and how to include, exclude or cut molecules at the packing boundaries.
- Page "Define Range" to define the boundaries of the parallel epiped. You may also define a sphere instead of a parallel epiped.
- Option to fill a slab or slice parallel to an hkl plane (compare command "Build/Fill/Slab"), with the cell range as delimiters.

Inserting (dummy) atoms and bonds
Using dummy atoms as centroids or as centers of coordination polyhedra:
- About dummy atoms and bonds
- Inserting an atom
- Dummy atoms as centers for coordination polyhedra
- About centroids
- Creating big bulbs in MOF frameworks

Connectivity, part 2: H-bonds and non-bonding contacts
- Three pages on Connectivity dialog: Consideration of connection parameters for bonds as well as for H-bonds and contacts.
- Support for multiple sets of H-bond and contact definitions: Contact and H-bond definition groups -- as there are "Standard contacts" and "Standard H-bonds", rsp., defined between the atom group pairs (like bonds are) and using van der Waals radii sum plus an offset as default.
- User-defined, special contact definition groups and H-bond definition groups, rsp. These may be defined on atom site level.
- Reported contacts/H-bonds (from connection parameters) are compiled in "Reported contacts" and "Reported H-bonds" definition groups, rsp., each.

Creating H-bonds and contacts directly from connection parameters
- "Build/Add All Atoms and Connections" also considers bonds, H-bonds, and contact parameters. This is a quick-and-easy option to create all atoms mentioned in the connection parameters, usually derived from _geom_xxx input loops as well as the bonds, H-bonds, and contacts between, as far as defined.
- Commands to add bonds, contacts or H-bonds from the context menu of the corresponding connection parameters tables.
- Commands in contact parameter table to expand to next atom or molecule.

Expand or reduce clusters of molecules
Use intramolecular contacts or H-bond definitions to find neighbouring molecules
- Dialog "Build/Expand" with several settings if to apply to all atoms or selected atoms or selected molecules, to enable intramolecular contacts, to regard H-bond definitions, too, and what to do with the contacted neighbouring atoms (broken-off bonds around or complete fragments).
- "Settings" page in that dialog, so you can choose the current connectivity settings or use different contact spheres, either relative to van der Waals radii or in absolute Angstroem boundaries.
- Push buttons to do expansion step-by-step: Add contacts now, Expand now. Push buttons to remove contacts or fragments, that means to step back.
- Command "Expand" from table of contact parameters: [Whatsnew_connection-parameters.htm, last part]
- Dialog "Build/Reduce" to remove molecules step-by-step, either the farmost molecules or all neighbouring molecules. Several settings to apply to or to start from and if and how to consider H-bonds and contacts.
- Accelerator keys and toolbar icons to expand or to reduce: "Create atoms' neighbouring atoms", "Create molecules' neighbouring atoms", "Create neighbouring molecules", and "Reduce directly".

Grow or cut molecular fragments or polymers
Add spheres to molecular fragments or to polymers step-by-step or remove them
- Command "Build/Grow or Cut": Apply to all or selected atoms (molecules or polymers), option to step over broken-off bonds.
- Also available from "Build" toolbar: "Grow directly" and "Cut directly".

Pump Up or Shrink Polymeric Frameworks
Suitable for polymers: Pump up or shrink multiple coordination spheres around selected atoms
- Pumping directly adds another coordination sphere around the currently selected central atom(s), even if there are already one or more completed coordination spheres around. That means Diamond adds atoms around the atoms of the (currently) farmost coordination sphere around the central atom(s).
- Shrinking directly removes atoms from the farmost coordination sphere around the selected central atom(s).
- Available as push buttons "Pump now" and "Shrink now" from within "Coordination Spheres" dialog or to perform directly from the dropdown menu of the "Fill coordination spheres directly" button in the "Build" toolbar.

Using the mouse wheel
- Blow up coordination spheres/polyhedra.
- Find non-bonding contacts.
- Expand molecules to clusters.

Destroying all or parts of the structure picture
Dismantling: overview.
Deleting atoms or bonds.
Deleting molecules or fragments.
Keeping the selected atoms, bond, or molecules but deleting the unselected ones.
Destroying the structure picture.

Display of structure picture

Rendered and flat representation
Rendered Representation: Overview
Rendered Representation: Features and Limitations
Switching Rendering On or Off

Models
Models: Overview
Switching the model
Model and Radii dialog
Ball-and-stick model (regular model)
Ellipsoid model
Wire model
Using Sticks Instead of Thin Wires
Space-Filling Model
Superimposition of Space-Filling Model
Individual assignment of models
Scaling all or selected atoms' or bonds' radii

Projection
Projection: Overview
Parallel and Central Projection
Enlargement Factor
Adjusting the Structure
Viewing Distance
Distortion of Atoms and Bonds
Changing Enlargement Factor or Viewing Distance With Mouse or Cursor
Zooming a Rectangular Area
Stereo Representation

Orientation and Position
Orientation: Overview
Center of Rotation
Orientation and Position
Rotating and Shifting the Structure (mouse, keyboard or by defining incremental values)
Viewing Along Selected Axes
Viewing Towards a Plane Given By Miller Indexes h,k,l
Continuous Rotation ("Rock and Roll")

Layout
Bitmap layout and page layout vs. normal layout
Difference between page layout and print preview
How to use a grid for the positioning of objects and to estimate the size of the structure window or printout page
How to use the Zoom function to scale a bitmap or printout page in the structure window
About double buffering

Background
Black-on-White Mode
Background Color
Transparent background

Lighting
Lighting: Overview
Lighting Effects for Standard Representation
Lighting Effects for Rendered Representation

Other effects
Other Effects: Overview
Depth Cueing
Shading Edge
Front Emphasizing
Bond Tapering
Overall Radius Factor

Designing atoms
Editing design, radii, and other properties for the atom groups and sites
Editing design, radii, and other properties for individual atoms ("created atoms")
Defining material properties for rendered representation
Copying the style of an atom and pasting it to selected atoms
Using the mouse wheel to change atom radii.

Designing bonds and contacts
Editing design, radii, and other properties for the bond groups and other connection types
Editing design, radii, and other properties for individual bonds and contacts
About thin and thick bonds, fragmentated bonds, and the design and relative length of broken-off bonds
Defining material properties for rendered representation
Copying the style of a bond or contact atom and pasting it to selected bonds and contacts
Using the mouse wheel to change bond radii.

Drawing ellipsoids
Styles of thermal ellipsoids
Displacement Parameters and Ellipsoid Representation
Exclude Selected Atom Types From Ellipsoid Representation
Rendering ellipsoid styles

Representation of mixed and defect sites
Choosing how to display the components of a mixed site
Definition of colors for mixed site representation
Setting the opacity to site occupation factor (S.O.F.)
Using random distribution of mixed site components

Color differentiation
Differentiate atom colors for: Charges/oxidation numbers, site occupation factors, symmetry operations, Bravais translations, cell translations, or Wyckoff positions.

Anti-aliasing
Using anti-aliasing to get smoother edges when rendering atom, ellipsoid, bond etc. objects
Changing the resolution of rendered objects
Temporarily reducing the resolution (and increasing the frame rate) when rotating or shifting in tracking or grab mode.

Unit cell vectors a, b, c, and atom vectors
Displaying the Unit Cell Axes
Vectors can be assigned to atoms, e.g. to indicate a magnetic moment.

Labelling atoms and bonds
Labelling Atoms and Bonds: Overview
Adding Labels
Atom Label Text
Bond Label Text
Style, Size, and Position
Shifting Label Position With Mouse or Cursor
Changing Label Text, Size, or Style After Creation
Removing Labels

Adding text to structure picture
Text: Overview
Adding Text
Contents of Text String
About control characters in text strings
Using Text Fields
About control characters in text strings
Style, Size, and Position
Shifting Text Position With Mouse or Cursor
Changing Text, Style, or Size After Creation
Removing Text

Legend of atom groups
Settings (position, atom sizes, font etc.)
Relative vs. absolute positioning

Coordinate system
Settings (position, axes lengths, font etc.)
Relative vs. absolute positioning

Plane and line objects
Planes can be defined by hkl or as (best) plane through a set of three or more atoms (or a line through two or more atoms).
Creating plane and line objects.
Tables and properties of plane and line objects.
Checking the planarity or linearity.
Editing or destroying plane or line objects is available through the "Objects" main menu. Additionally editing or deleting (L.S.) planes or lines through atoms is possible directly from the constituent atoms.

Polyhedra

Polyhedra Overview
- Overview of polyhedron functions
- Features and limitations

Creating Coordination Polyhedra
- Semi-automatic vs. manual creation
- Selecting Atom Types
- Using Fixed or Generic Spheres
- Define polyhedron's constituent atoms from atom site environment and define polyhedron prototypes for atom sites.
- Take the neighbouring atoms as is without complementing the missing neighbouring atoms inside the sphere boundaries.
- Getting Polygons Greater Than Triangles

Polyhedra with no central atom
- Getting the dummy atom
- Cubes and other 3D objects without central atom inside

Polyhedron construction from atoms and bonds
- Construct Polyhedron dialog
- Construct one single polyhedron from selected atoms
- Choose a central atom or define a dummy atom
- Options if and how to consider bonds between the ligand atoms to be considered as polygon edges

Creating polygons
How to create polygons using centroids, e.g. in phenyl rings

Polyhedron design and hatching
- Design and Material Properties
- Hatching
- Displaying Polyhedra With Front Faces Open
- Global Settings For All Polyhedra

Polyhedron selection and properties
- Selecting a polyhedron from the structure picture
- Choosing a polyhedron from the Table of Polyhedra
- Polyhedron in Properties view

Modification and duplication of polyhedra
- Changing designs after creation
- Removing unwanted edges or adding edges to a polyhedron.
- Copying a polyhedron building to other atoms of the same atom site.

Creating Voronoi polyhedra
- Voronoi polyhedra can be created for selected atoms or atoms of selected sites basing upon their Dirichlet domains.
- There are several options for the style of the polyhedron as well as if and how to show and connect the neighbouring atoms.
- Infos about a selected Voronoi polyhedron (neighbouring atoms, distances, bond strengths, solid angles, etc.) are available from the Properties view.

Destroying polyhedra
About destroying single or all polyhedra from the structure picture

Distances and angles

Table of distances and angles
- Showing the distances and angles table
- Settings for distances and angles table
- Selecting between distances and angles calculation
- Configuring the format of the table of distances and angles
- Selecting an atom in the structure picture can highlight the corresponding atom of parameter list in distances table
- Distances histogram in the Properties pane.

Distances around a selected atom
- Table of distances around one or more selected atoms
- Matrix of distances between selected atoms
- Histogram of distances around atoms or between atoms
- Settings for table (dmin ... dmax) and histogram (dmax).

Measuring and reporting distances, angles, and torsion angles
- Measuring distances, angles, and torsion angles
- About reported distances, angles, and torsion angles
- Measuring distances etc. between centroids (dummy atoms).

Extended geometric infos: Angles between planes etc.
- Distances of atoms from planes or lines as well as angles between planes and/or lines can be measured interactively.
- Calculating angles between plane and/or line objects.
- Calculating distances of atoms from a plane or line object.
- Table of extended geometric infos.
- Extended geometric infos in the data sheet.

Copying, saving, and printing distances and angles informations
- Copying, saving, and printing or previewing the table of distances or angles
- Application to tables of reported distances, angles, and torsion angles
- Copying, saving, and printing or previewing distance information in the properties pane.

Data sheet and powder pattern

Data sheet contents
- Brief and comprehensive configuration
- Data Sheet Settings dialog.

Customizing a data sheet
Besides the options "brief" and "comprehensive", the data sheet can be customized by the user, i.e. the selection and order of the items as well as a few more options can be changed.

Powder pattern simulation
Powder diffraction data can be calculated and displayed in both table and diagram and update automatically when structure parameters change.
- Activating the powder pattern view
- Powder pattern settings
- Diffraction diagram settings.

Copying, Saving, and Printing Data from the Data Sheet or Powder Pattern
- Copying (parts of) the data sheet to the Windows clipboard.
- Printing or previewing the data sheet.
- Copying rows of the table of reflection parameters to the Windows clipboard.
- Saving (or exporting) the reflection parameters.
- Saving (or exporting) the contents of the reflection parameter table as plain text.
- Printing or previewing the reflection parameter table.
- Copying the diffraction diagram as bitmap to the Windows clipboard.
- Printing or previewing the diffraction diagram.

Printing, copying, and exporting structure pictures

Printing a structure picture
- Setting the page format
- Page View and Print Preview to control the page format
- Banding of rendered pictures
- Printing using Print dialog
- Printing directly

Copying the Contents of the Structure Picture
- Using the regular Copy command
- Using Copy Graphics command

Saving the Structure Picture as 2D Image File
- Saving the Structure Picture as Metafile or in a bitmap format (BMP, GIF, JPG, PNG, or TIFF)
- Using the Export command

Creating video sequences or image series
- Video sequences can be recorded to create e.g. AVI video files or a series of single images.
- Tools/Take Image command to add single images, e.g. to save later as a series of image files, or to generate a video later, using Tools/Save Images.
- Frame selection in video sequence creation.

Exporting 3D structure picture data
The contents of a structure picture can be exported as 3D model into the formats OBJ (Wavefront), STL, and VRML via the command "File/Save As/Save Graphics As..." or via "File/Export...".

Creating POV-Ray scenes
The POV-Ray assistant helps you to create photo-realistic pictures for this outstanding, free available ray-tracer, with features like textures, background, ray-tracing, multiple light sources, etc.
- Setup of POV-Ray
- Running a POV-Ray preview
- Where to find POV-Ray settings
- Exporting a POV-Ray picture
- POV-Ray tutorial

POV-Ray animations and video sequences
There are several commands in the "Tools/POV-Ray" submenu that deal with animations and image sequences:
- "Start Recording POV-Ray Sequence" creates a series of POV-Ray scene files, a series of image files, or a video file (or all of them) from the pictures that Diamond has recorded between an initializing "Start Recording POV-Ray Sequence" and a terminating "Stop Sequence" command.
- "Create Sequence from Pictures" works similar to the above commands but it does not compile from recorded pictures but from the pictures that are marked as selected in the thumbnails overview when you call the command.
- "Animated POV-Ray Scene" runs POV-Ray to create a series of images or a video from a rotation or shift animation applied to a single structure picture.