Diamond Version 5 User Manual: Automatic, assisted, and manual picture creation

Picture Creation Assistant

This optional assistant helps you to create or modify a structure picture in a few steps

In this article:
- Overview of the Picture Creation Assistant
- 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

Previous article: Automatic vs. manual picture creation
Next article: Auto Picture Creator

Overview

The Picture Creation Assistant is a versatile tool that guides you through the individual steps of creating and designing a picture. It can be applied to a new blank picture as well as to an existing picture, e.g. to change a 3D rendered representation to a black-on-white printout.

It offers the most common building functions such as:

• adding atoms,
• creating a packing diagram,
• creating molecule(s) directy from the atomic parameter list,
• filling a cell range,
• filling coordination spheres or creating polyhedra.

Besides this it offers basic functions for the structure picture display and the viewing direction:

• defining the model (e.g. wires, ball-and-stick, space-filling, ellipsoid),
• defining the design of atoms and bonds,
• defining the layout of the structure picture (e.g. "Bitmap" or "A4" page),
• defining the initial viewing direction,
• and many others.

The Picture Creation Assistant is available from several commands that create a new structure data set or import data from a foreign file format and helps you to create your first picture or helps you to create a second, third, etc. one. It can be called directly from the Picture main menu using the Picture Creation Assistant command in order to start from a blank picture or to modify an already existing picture.

Where to start from

The Picture Creation Assistant is a multi-page dialog. On the first of it, the Welcome page, you decide to start your building from scratch or to make use of a building scheme or from a proposal of Diamond basing on the structural parameters.

If you call the assistant for a structure picture that has content - either built up manually or automatically with a proposal of Diamond, you have the choice to leave the current picture building unchanged. The Leave current picture building unchanged checkbox is set whenever you call this dialog for an already existing structure picture building. Leaving the checkmark set or setting it will directly lead you to the picture design settings page of the assistant.

If you decide to change the picture building -- or the picture is still empty --, you have the choice to select a building scheme from the combobox titled You can derive [...]. Or set the checkmark at Get a proposal from structural parameters, this is the building scheme suggestion from Diamond basing upon structural parameters. If you choose the proposal or a building scheme, the following pages referring to the picture building settings will then reflect the content of the selected building scheme.

Note: Building schemes are handled in one of the following articles. The article "Optimizing the Representation of the Structure Picture" describes how to apply the Picture Creation Assistant to modify an already existing picture, e.g. for publishing.

The Next button brings you to the basic building options, if you start from a blank picture (or destroy existing picture contents), or directly to the first design settings page.

Basic building functions

On the second page of the assistant you decide about the so-called "picture building basics" (or "primary atoms"), i.e. which atoms shall be created before any of the building operations on the following pages of the assistant are carried out.

In the general case (meaning if we did not use the "Packing diagram 1" building scheme on the Welcome page), the default basic settings are to fill the contents of the unit cell. For the screenshot below we change the Range option to "Quadruple cell XY", filling the unit cell as well as three neighbouring cells. The boundaries in crystal coordinates are adjusted as well.

Other options are:

Adding all atoms (and optionally bonds, H-bonds, and contacts)
This option adds all atoms of the parameter list to the active structure picture. If the structure is a crystal structure, no symmetry operations or cell translations are applied.
By default, the option (checkbox) Add all bonds is also activated, meaning that all bonds from the bond parameter list will be created along with their associated atoms each (which may have additional symmetry operations and cell translations).
To create all H-bonds and non-bonding contacts from their corresponding connection parameter lists, including associated atoms, activate the checkboxes Add all H-bonds and Add all non-bonding contacts, rsp.

Creating molecules directly from the atomic parameter list
The option Get molecules [...] creates one or more molecules directly from scratch based on the atomic parameter list. For a crystal structure, Diamond applies symmetry operations and/or cell translations, if necessary to get complete molecules rather than a scattering of fragments or vagabonding atoms, if the coordinates in the atomic parameter list do not describe entire molecules.
If the structure is polymeric - or the connectivity settings need to be adjusted - the molecular generator stops when it encounters the same atom/bond patterns in neighbouring cells.

Creating a packing diagram
The packing diagram option is described below.

Creating no basic atoms
It is also possible to skip the creation of "primary" (initial) atoms using the option None of the above mentioned. It is generally appropriate, if your structure picture already contains atoms and you use the Structure Picture Creation Assistant to modify your picture, e.g. add coordination spheres or polyhedra.

Note: All building options in the Picture Creation Assistant are also available through corresponding manual building functions. The section "Building up structural parts" of the Diamond User Manual describes the functions to build up a structure in more details.

On the next page you define, if and how far to add cell edges, bonds, or polyhedra to the picture building.

Adding additional atoms, bonds, or polyhedra

On the third page of the assistant you can define additional atoms and bonds as well as cell edges and coordination polyhedra on top of the previously defined basics:

There are several options that can be used in combination:

Creating cell edges
Setting the checkmark at the Create cell egdes checkbox draws the edges of the unit cell. If you have selected to fill more than a single unit cell on the previous page, the edges of all filled cells will be drawn.

Connecting atoms
If you check this option, the atoms in the structure picture will be connected by bonds, based on the current connectivity settings.

Filling coordination spheres
If the Fill coordination spheres checkbox is activated, all atoms within the coordination spheres around currently present atoms, e.g. the "primary atoms" defined on the previous page or in an already existing picture, of elements given in the Central atom elements list will be created. The sizes of the coordination spheres depend on the current connectivity settings. This step will be repeated Cycle count times.

Creating coordination polyhedra
If the Creating polyhedra around checkbox is activated, coordination polyhedra around all atoms of elements given in the list to the right will be built. The sizes of the coordination spheres depend on the current connectivity settings. If you are using the Structure Picture Creation Assistant on an existing structure picture, you can use the Destroy existing polyhedra checkbox to remove any existing polyhedra before Diamond creates new ones.

Completing molecular fragments
If this checkbox is activated, molecular fragments that have been cut during the primary atom creation on the previous page (or in an existing picture) will be completed. The current connectivity settings are used as a guide to determine bonded atoms.

Creating broken-off bonds
If a crystal structure is "polymeric" (i.e. does not only consist of finite molecules), there are necessarily some bonds at the borders of the currently displayed structure part which point to the hypothetical next atoms just outside this structure part. If this checkbox is checked, the bonds to these hypothetical ligand atoms will be drawn shorter than common bonds ("broken-off bonds"). These bonds pointing into space are often used to illustrate infinite structures.

The page opened by clicking the Next button defines the drawing target and the basic design of atoms and bonds. But below we first explain the option to create a packing diagram.

Creating a packing diagram

A packing diagram is generally more appropriate for crystal structures consisting of finite molecules than for three-dimensional frameworks. If you choose Create packing diagram as building basics, you define the size of the cell range with the Range checkbox or with the six fields X-min through Z-max. (The default cell range is the unit cell.) Diamond fills the cell range with molecules and/or vagabonding atoms and/or atoms of polymeric structural parts. The choices how and which molecules to include in the cell range will then follow on the subsequent page of this assistant.

If you choose Create packing diagram as building basics, the assistant will lead you to an alternative third page with special settings for the packing diagram. Otherwise the third page is the (above mentioned) page "Additional atoms and other objects", that means if and how to fill coordination spheres, create polyhedra, connect atoms, etc.

The How to include molecules in the packing group of options (radio buttons) defines if and how to include or cut molecules in the cell range given on the previous page of the assistant:

Include a molecule completely, if its reference position fits [...]
This is the default option. It considers a molecule only, if its reference position fits the cell range. The default for this reference position is the center of the molecule, that means the mean value of the (x, y, z) positions of all associated atoms of the molecule. In most cases, this means that a molecule is considered, if most parts of it are inside the cell range, but is not, if most parts are outside.

Include a molecule completely, if any of its atoms fit
This option considers every molecule, if at least one of its associated atoms lies inside the cell range. In most cases, this option yields the packing with the most molecules, that means a lot of molecules hanging (almost completely) outside the cell range - besides the molecules that are completely inside the cell range.

Include a molecule completely only, if all of its atoms fit
This option considers a molecule only, if all of its atoms fit in the cell range. This option yields a packing with relative few molecules, since all other molecules hanging (more or less) outside the cell range are skipped.

Cut both molecules and polymers at cell range boundaries
This option cuts those parts of the molecules that are hanging outside the cell range. With other words, this option just fills the cell range with atoms and connects them, regardless, if there are molecules cut, or if it is a polymer.

The other options Create broken-off bonds, Create cell edges, and Create polyhedra around work in the same way as described above under "Adding additional atoms, bonds, or polyhedra".

Screenshot of page with packing diagram settings when "Create packing diagram" has been selected in previous page

Defining the picture design

The fourth page handles the picture design. Here you define the basic design settings of the picture like the model, the layout (bitmap, A4 page etc.) and the format (rendered representation, gray-scaled etc.). It also allows you to choose a design scheme (cf. article "Definition and application of design schemes (style sheets)").

If you want to use a design scheme, choose one from the combobox Scheme. The settings below will adjust to the corresponding settings defined in the selected scheme. The screenshot below uses the design scheme "Ellipsoid plot, colored", which is defined in the article "Definition and application of design schemes (style sheets)" in the chapter "Scenario 2: Quick definition and application of a design scheme".

If you do not want to use a design scheme, choose the option "(No design scheme)". (This or simply a blank field is the default option.)

Model etc.
Diamond provides a variety of models, like "ball-and-stick", "space-filling", "wires" and "ellipsoids". Normally, the model can be selected for all atoms or also for individual selected atoms using the Model and Radii..." command in the Display menu. In the Structure Picture Creation Assistant, the most common combinations of these models along with typical design settings (like two-colored bonds) can be selected using the "Model etc." combobox.
Note: If you would like to keep the current setting, you should select "(No changes)".

Layout
In this combobox, you can select the destination of the structure picture:

• If you would like to create it only on the screen, "Windows (variable size)" is generally most appropriate.
• If you would like to create a bitmap which shall be exported to be used in other programs, you should select one of the "Bitmap" lines with an appropriate resolution.
• If you would like to create a picture for printing, please select the size of your paper at the bottom of the list.

Format
This option provides some sort of quick design settings for various purposes. For example, while you normally would of course select "Rendered (highest quality)" while working at your computer, you can use the option "Gray-scaled" for quickly creating a picture suitable for a printed publication.
If the selection for "Format" is not "(No changes), you can also apply the "Avoid duplicate atom main colors" option. If this option is checked, Diamond will try to find different atom colors for each atom group.

Note: The picture design and viewing options in the Picture Creation Assistant are also available through corresponding manual functions. The section "Display of structure picture" of the Diamond User Manual describes these functions in more details.

Choosing viewing direction and projection

On the fifth page of the Picture Creation Assistant you define the viewing direction, i.e. the orientation of the crystallographic axes a, b, c (or the axes of the orthogonal coordinate system, if it is not a crystal structure) relative to the axes of the view coordinate system. Besides this you can choose between parallel and central projection (perspective) and if to adjust the structure picture's dimensions automatically to the boundaries of the drawing area.

Note: The articles "Projection" and "Orientation and position" describe in more details how a structure picture is projected to the drawing area.

Viewing direction
You can select the direction in which you would like to view at the structural model. Options are e.g. to view along a certain unit cell axis, along a face or space diagonal, along some axis given by [U,V,W], or towards a certain plane defined by (hkl). Besides this, you can also let Diamond select the viewing direction automatically ("best projection").
If you would like to change the viewing direction later on without the assistant, please select the corresponding command form the Display menu.

If you choose to view along a crystallographic (or orthogonal) axis or a special axis or towards a plane, you can rotate the structure picture for some degrees by defining the angles in the Tilt [...] input fields.

Projection
You can choose between "Parallel projection" and "Central projection (perspective)". While the first one is generally more appropriate for working with the structural model (you can e.g. select atoms more easily), the perspective impression is better for creating photorealistic POV-Ray(TM) images as well as video sequences.
You can change the projection also without the assistant on the corresponding page of the Display/Representation... dialog.

Adjust enlargement factor and position to fit...
If you choose this option, the Automatic Adjustment as well as the Automatic Centering will be activated. As a result, the center of rotation will automatically be placed in the center of the screen; besides this, the enlargement factor" is automatically adjusted so that the complete structural model is visible on the screen.

Defining additional objects

The sixth (and last) page of the Picture Creation Assistant can be used for additional objects like the legend of atom types and the coordinate system showing the current orientation:

For both legend and coordinate system you have the choice to leave the current settings unchanged, to switch the legend or coordinate system, rsp., on or off (and leaving the position unchanged), or use "Show at ..." to show the object at a special position relative to the boundaries of the drawing area.

You can switch to the previous page (viewing direction) of the Structure Picture Creation Assistant or to any of the previous pages using the Back button and come back using the Next button.

The Finish button closes the assistant and performs all currently selected building and design operations. Note: The result of this operation will depend on the settings on all pages of the assistant, even if you have not visited them yet.

Previous article: Automatic vs. manual picture creation
Next article: Auto Picture Creator