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

Definition and Application of "Design Schemes"

Design schemes are some kind of style sheets with design and viewing settings to be applied to structure pictures

Design schemes in brief:
- 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...".
- Definition: Title, select which settings to save in the new design scheme. In the "Design Scheme" dialog you can make changes to the current settings before you save it as a new design, e.g. "Atom Design Properties" dialog, called from "Edit" dropdown menu.
- "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).

Previous article: Building schemes
Next article: Optimizing the Representation of the Structure Picture

Definition of a design scheme
A "design scheme" contains some basic picture design settings plus optionally the whole current design and viewing settings of a structure picture. The basic picture design settings as well as the viewing settings are already known from the "Picture Creation Assistant" that is in use since Diamond version 3.

You find the commands that deal with design schemes in the corresponding submenu of the Display menu. The first command Create Design Scheme From Picture... initializes a design scheme from the current picture settings -- from layout, model, rendering or not, across the atom, bond etc. designs up to the viewing direction. Use the checkboxes to decide what the new design scheme may change when applied later. For instance, you can create a design scheme that only reflects the atom (type) designs. So you can easily change current atoms' designs to have different colors, ellipsoid styles, etc.

The second command Create Design Scheme From Selection... (introduced in version 5.1) does not access the global picture settings but the designs of the atoms that are currently marked as selected as well as the designs of the selected bonds, contacts, and H-bonds and the designs (of faces and edges) of the currently selected polyhedra. This is well suited to create design schemes for special building units, e.g. inorganic units with complex polyhedra or molecular fragments.

We show the definition and application of design schemes in the following scenarios. Scenarios #1 through #3 work with global picture settings, while scenario #4 demonstrates how to define a design scheme from the atoms and bonds of a selected molecular fragment that can be used as organic linker in Metal Organic Frameworks (MOF).

Scenario 1: Defining a design scheme and applying to another structure

The following screenshot shows the Design Scheme dialog. Open the sample file "PCD-V5O9-LT-1250105.diamdoc", which contains one picture with a unit cell viewed along c-axis and with semi-transparent coordination polyhedra around all V atoms.

Defining the design scheme
At top there is the title that will be assigned to that (new) design scheme.

In the next section you find the basic settings with options that you already know from the "Picture Creation Assistant", concerning:
- Layout (if you target a window, a bitmap or a printout page and some bitmap/page sizes).
- Model etc. (Wires or sticks or ball-and-stick or space-filling, with options for mono- or two-colored bonds).
- Format (high-quality rendering with lighting or flat with or without light bulbs or even just black-on-white sketch).
- Avoid duplicate atom main colors: This alters (when checked) colors to avoid that two or more atom types use the same color.

The third section enables storing of individual settings concerning the picture design of the current picture - provided that the corresponding checkmark is set. These are:
- The colors of elements or atom types, the styles of atom types or elements, and the radii of atom types or elements. This means you can store the mentioned atom design properties in the design scheme to re-assign them later to another structure, for instance you can create a design scheme where oxygen atoms are pink rather than (default) red or so.
- Analogously you can save the default designs for bonds, contacts, H-bonds, broken-off bonds as well as the default design for polyhedra in the design scheme to apply it later in another structure picture.
- General global display settings. These are settings that are (most of them) defined under Display -> Picture Settings...
- Settings for objects like legend (of atom types) and the coordinate system (which shows the current orientation).

The fourth section is for viewing direction and projection, and has already been available in "Picture Creation Assistant" since Diamond version 3.

Before we save this design scheme as new design scheme with the title "Test from V5O9 sample" in the Windows Registry, we will point you to some additional possibilities to make changes - for instance in atom, bond, and polyhedron designs. Push the Edit menu button (in the Design Scheme dialog), which opens a menu with commands to edit atoms' (better: the atom types' or elements') colors, styles, and/or radii as well as properties of bonds and bond-like objects and polyhedra.

Note: Some screenshots in this article have been made with version 4 of Diamond.

Commands Atom Colors..., Atom Styles..., and Atom Radii... open the Atom Design Properties dialog, which begins with two rows, one for "V+0" and one for "O+0". If you want not only V but e.g. also Nb and Ta to become lime green when assigning the design scheme "Test from V5O9 sample", you can edit the element (or atom type) in the corresponding table cell. The same works for atom types' (or elements') styles and radii on the other two pages Styles and Radii, rsp. (here not depicted).

Application of a design scheme
We now close the document and open another sample document "PCD-Ta2O5-1250377.diamdoc" and assign the previously defined design scheme to that structure picture.

The Ta atoms and the bonds are light gray (color delivered from Diamond export from Pearson's Crystal Data) and turn -- after application of the design scheme -- into lime green (Ta) and yellow (bonds), rsp. (To change the coordination polyhedra, we have to call Display -> Polyhedron Designs..., ensure that the Update existing polyhedra checkmark is set and confirm with OK.)

"Apply Design Scheme" dialog
Besides this direct application method, you can run the command Display -> Design Schemes -> Apply Design Scheme... and choose the design scheme (here: "Test from V5O9 sample") and remove checkmarks from the design sections and fields you don't want to be changed, for instance when you remove the checkmark at Standard polyhedron design [...], the standard polyhedron design in "PCD-Ta2O5-1250377.diamdoc" would be left unchanged.

Two ways of creating a design scheme
(1) Make your preferred picture design settings manually by using several commands from the Display menu, typically Model, Atom Designs, Picture Settings, etc. Then run Create Design Scheme from the Design Schemes sub-menu of the Display menu. In the dialog (see example above), you may choose which fields of the scheme to be relevant. (In the above example: all fields including picture viewing settings.) Give your scheme a title and save it.

(2) Use the "Auto Picture Creator" to approach your preferred design by changing settings for Layout, Model etc., and Format in the Picture design category, and then run Create Design Scheme dialog like described under (1).

Design Scheme Manager
The Design Scheme Manager -- see Tools menu -- is available independent from a (current) structure picture and allows you to maintain, add, edit or delete design schemes whereever later It will also allow you to import and export resources for element colors, atom type styles, and radii -- but this will not yet be available in the first versions of Diamond 5. Delete is already possible to remove the highlighted design scheme from the list (and the Windows Registry and the Display/Design Schemes sub-menu).

The Settings in the lower part of the dialog define, if and how far you will be prompted, if there are ambiguities when creating a design scheme from selected atoms etc. and where to apply a design scheme, if there are currently selected objects in the structure picture.

Scenario 2: Quick definition and application of a design scheme

Make your structure picture settings (a rendered colorful screen plot or an ORTEP-like ellipsoid sketch on white paper) along with the designs of atom (groups, sites), bonds, polyhedra, etc. -- and simply call Create Design Scheme to create a design scheme from these current picture settings and save it under a title, so you can access this scheme whenever you later want to quickly re-design a picture from another structure.

The following example shows how to quickly re-design a rendered color picture to a flat color-line ellipsoid sketch on a white A4 page. After loading sample file "COD-1004001.diamdoc", which begins with picture "Molecule, viewed along b-axis":

The default or current setting is "window layout", "ball-and-stick model" and "rendered". We run the command Display -> Design Schemes -> Create Design Scheme... and make the following settings in order to get a design scheme for an A4 printout page, thermal ellipsoids, and flat color line representation:

We call this design scheme "Ellipsoid plot, colored". Ensure that the checkmarks are set in Layout, Model etc., Format and Avoid duplicate atom main colors and the other checkmarks are cleared. Then store this design scheme with OK.

Application of a design scheme that has been created previously titled "Ellipsoid plot, colored" will now be applied to the structure picture "Molecule, viewed along b-axis" resulting in this page layout with white background and black outlined bonds and atoms in ellipsoid representation:

Well, this could be easier done with a function like Picture -> Picture Creation Assistant (leaving picture building and viewing direction unchanged but setting the options on the picture design page as stated above. But we want to apply the design scheme now to another picture, and maybe later to more pictures, whenever we want to have a flat-looking color printout in A4 size.

Switching to the second picture in the document, entitled with "Two molecules" ...

... applying design scheme "Ellipsoid plot, colored" leads to:

When using the "Auto Picture Creator", the simplest way is to choose the design scheme from the "Scheme" combobox in the "Picture design" section of the Auto Picture Creator. Other ways -- if you prefer manual changes at your structure picture -- is to choose the appropriate design scheme from the Design Schemes sub-menu in the Display menu. When running Apply Design Scheme from a Design Scheme dialog, you have additional choices which fields of the scheme to apply, e.g. just the atom and bond desings but leaving rendering options and background color settings unchanged.

Scenario 3: Using design schemes to create atom color, style and radii resources

The most convenient way to create a design scheme is from an existing structure picture. The scenario 3 part of the article shows you how to derive a set of resources for atom main colors, atom styles, and radii.

Since there are a lot of settings that affect the appearance of a structure picture, such as layout, background color, rendered or flat, enlargement factor etc., the easiest way to create a design scheme is to build a structure picture, and then to call the Create Design Scheme command from the Design Schemes sub-menu in the Display menu.

The disadvantage is that you have just a small subset of different elements or atom types in your structure. If you take the design scheme created from that structure and apply it to another structure but with different elements, these other elements' colors (and styles and radii) would not be affected by the design scheme. The screen shot below (sample "COD-7103386.diamdoc") shows the design scheme settings dialog and the set of atom main colors generated from that structure - here just Pt, S, P, N, O, F, C, and H.

To extend the definition of atom main colors, atom styles, and radii for ball and space-filling representation to other elements than just Pt, S, P, N, O, F, C, and H,, run Edit in the Design Scheme dialog. Enter the element symbols in the corresponding row of the Elements or atom types column and confirm with OK, example below:

Give this design scheme an appropriate title and assign it later to structures containing similar elements, e.g. Cl instead of F, or Se or Te instead of S, etc.

Scenario 4: Creating design schemes for organic linkers

The best way to create design schemes for special building units like complex polyhedra or molecular fragments that are part of a complex (metal-)organic framework is to start from a set of selected atoms, bonds, and if necessary polyhedra. Here we show how to define a design scheme for terephtalic acid, which is an organic linker in many metal-organic frameworks (MOF).

Creating the design scheme
We create the design scheme from the MOF-5 compound COD-1516287 (sample file "cod-1516287-MOF-5-280-K.diamdoc"), where we
- select the 16 atoms (C, H, O) of the terephtalic acid unit including the 16 bonds between the atoms (left side),
- use the commands Atom Design and Bond and Contact Design from the Display menu to change the fill colors to "light blue",
- then call the Create Design Scheme From Selection command in the Display/Design Scheme sub-menu
- and change the title for the new design scheme in the Create Design Scheme dialog to "Terephtalic acid".

Checking the main colors of the elements of the selected atoms (C, H, O) by using the Edit dropdown button shows they use the same color in the design scheme:

We close the Create Design Scheme dialog with OK. The design scheme "Terephtalic acid" will now be available through the Design Scheme Manager and the Apply Design Scheme dialog.

Applying the design scheme
When we later want to design another MOF compound that also has terephtalic acid as organic linkers, we:
- choose one of the complete terephtalic acid units and ensure that all 16 C, H, and O atoms and the 16 bonds between are selected,
- use the command Edit/Extended Selection/Select Symmetry-Related to select all (symmetry-related) terephtalic units,
- choose the command Apply "Terephtalic acid" from the Display/Design Scheme sub-menu.

This will prompt you if you want to apply the selected design scheme (here: "Terephtalic acid") to the current selection or to the whole picture. Choose "Yes".

An alternative is to choose the command Apply Design Scheme... where you can choose your design scheme from the Design schemes dropdown list at the top of the dialog and choose your target option from the Apply to dropdown list at the bottom of the dialog. The advantage is that you can disable unwanted properties when applying a design scheme. As you see, some of the properties are greyed out. This is because you have created the design scheme from selection rather than from the whole picture and thus these general properties have not been included:

Note: Design schemes created from selected atoms, bonds, and/or polyhedra are not limited to the structural unit where they have been created from. So you can apply a design scheme such as "Terephtalic acid" to all organic linkers (or molecular or polymeric units in general) containing C, H, and O.

Previous article: Building schemes
Next article: Optimizing the Representation of the Structure Picture

References:
PCD:1250105: V5O9 LT in P-1.
Le Page Y., Bordet P., Marezio M.; "Valence Ordering in V5O9 Below 120 K"; Journal of Solid State Chemistry, 92, 380-385 (1991).
PCD:1250377: Ta₂O₅ rt orth3 ("L-Ta2O5") in Pmm2 (25).
Stephenson N.C., Roth R.S.; "Structural Systematics in the Binary System Ta₂O₅-WO₃. V. The Structure of the Low-Temperature Form of Tantalum Oxide L-Ta₂O₅ "; Acta Crystallogr. B (1971) 27, 1037-1044.
COD:1004001: Tungsten sulfide cluster with tri-n- (octakis(mu!3sulfido)-hexakis(tri-n-butylphosphine) -hexa-tungsten) by Jin, Song.; Zhou, Ran.; Scheuer, Ellen. M.; Adamchuk, Jennifer.; Rayburn, Lori. L.; DiSalvo, Francis. J.; Inorganic Chemistry, 40, 2666-2674 (2001).
COD:1516287: Elucidating Negative Thermal Expansion in MOF-5 by Lock, Nina; Wu, Yue; Christensen, Mogens; Cameron, Lisa J.; Peterson, Vanessa K.; Bridgeman, Adam J.; Kepert, Cameron J.; Iversen, Bo B.; The Journal of Physical Chemistry C, 114, 16181 (2010).
COD:7103386: Self-assembling squares with amino acid-decorated bipyridines: heterochiral self-sorting of dynamically interconverting diastereomers by: Rang, Alexander; Nieger, Martin; Engeser, Marianne; Lützen, Arne; Schalley, Christoph A; Chemical communications (Cambridge, England), *, 4789-4791 (2008).