Diamond Version 5 User Manual: Display of structure picture

Designing bonds and contacts

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Next article: Drawing ellipsoids

Like for atom groups, Diamond associates designs, radii, and other properties to each bond group, that means for each atom group combination. When bonds are created, each new bond will get the properties of the corresponding bond group. To get more information about "created" bonds and bond groups, see the article "About toms, Atom Groups, Bonds, and Bond Groups". The properties of every single created bond can be changed afterwards independent from its associated bond group.

This article describes:

·       How to edit design, radii, and other properties for the bond groupsmanual_display_bonddesign_bondtypes>manual of the current structure.

·       How to edit design, radii, and other properties for individual bonds or contactsmanual_display_bonddesign_bonds>manual.

·       About the difference between thin and thick bondsmanual_display_bonddesign_thinthick>manual.

·       About fragmentated bondsmanual_display_bonddesign_frag>manual.

·       Design and relative length of broken-off bonds.

·       How to design colors and stylesmanual_display_bonddesign_colorsstyles>manual (interior and edge) of a bond or bond group or contact design.

·       How to define material propertiesmanual_display_bonddesign_material>manual for rendered representation.

·       How to assign selected properties to multiple or all connection types or bond groupsmanual_display_bonddesign_assigntotypes>manual of the current structure picture.

• How to copymanual_display_bonddesign_copystyle>manual the style of a bond and paste it to selected bonds.

Designing Bond Groups

Like with atom groups and created atoms, the design, radius, and other properties of each bond group serves as basis for all created bonds associated with that bond group. That means you can assign properties to bonds according to the atom groups involved. When you alter the properties of one or more bond groups, these changes may overwrite the properties of all created bonds associated with those bond groups.

The command Bond and Contact Designs from the Display menu defines the design for bonds, H-bonds, broken-off bonds as well as for non-bonding contacts. If this command is run from the Display menu without any bonds being selected, the Bond Group Designs dialog will open where you can edit properties (e.g. style, colors, weight, etc.) for all bonds belonging to a certain bond group (= pair of atom groups). If at least one bond or contact is selected, you have the choice between the Bond Group Designs dialog and the Bond Design dialog, where the properties of the selected bonds (contacts) can be set. The latter is also true if you run the command in the Edit submenu of the context menu of selected bond(s)/contact(s).

The Bond Group Designs dialog offers two pages:

·       Style and Colors: Defines style, interior, edge, and radius properties.

·       Others: Defines global settings that apply to all bonds and bond-like objects.

The tree list Bond groups/Connection types is a list of all connection types (i.e. bonds and bond-like objects). The "bond groups" (i.e. atom group pairs) that are present in the structure picture are accessible when opening the "Default bond design" item (with the plus sign).

You can select "Default bond design" in order to change the default bond style for cases in which no bond style has been selected yet. Select "broken-off bonds", "H-bonds", "non-bonding contacts", or "other bond-like objects", if you want to change the styles for these connection types, rsp.

When opened for the first time, the "Style and Colors" page is shown for the default bond design

The "Style and Colors" page of the Bond Group Designs dialog for the selected bond group "Os+0"---"C+0"

Select the connection type or bond group you want to edit from the tree list Bond groups/connection types at the upper left of the dialog window, and make the changes on the Style and Colors page of the dialog as far as needed. You will find details about colors, styles, radius, etc. below in this article:

- Colors and Stylesmanual_display_atomdesign_colorsstyles>manual,

- Material Propertiesmanual_display_atomdesign_material>manual.

Updating existing bonds

By default, Diamond updates all created bonds (and H-bonds and contacts) when you close the Bond Group Designs dialog with OK. That means each created bond etc. gets the design of its associated bond group (or connection type), like it is done with atom groups and created atoms. To disable this automatic update mechanism, switch off the Update bonds etc. checkbox.

Defining a default bond style

While designs can be stored for every atom group in the Diamond section of the Windows Registry, bond group designs cannot. Instead, Diamond accesses a default bond design when creating new bond groups. You can define the default bond design by selecting the corresponding item in the list and adjusting the settings on the Style and Colors page.

Resetting connection type and bond group designs

This restores the designs of all bond groups of the current compound to the design selected as <Default bond design>, if "Default bond design" (or a bond group) is selected. If one of the other connection types is selected (e.g. "non-bonding contacts"), it resets the default designs for contacts, H-bonds and other bond-like objects, rsp., to factory settings.

Designing Selected Bonds

This part of this article describes how to edit the colors, style, radius, and material properties of a single bond or contact or of multiple selected bonds and/or contacts. These settings are defined in the Bond and Contact Designs dialog, which uses the same two pages as the above described Bond Group Designs dialog - but without the tree list of connection types and bond groups, since it refers to the currently selected bond(s) or contact(s) only.

Editing a single bond's or contact's properties

The easiest way to design a single bond or contact is to double-click on the bond or contact, rsp. Instead, you can click with the right mouse button on the bond/contact, and then choose the Edit -> Bond Design command from the context menu.

Editing properties for multiple bonds and/or contacts

Select the bonds and/or contacts you want to edit. There are several ways to select bonds; see the article "Selecting objects". Then click with the right mouse button into one of the selected bonds/contacts, and choose the Edit -> Bond Design command from the context menu.

As for selected atoms, properties which are not unique for all selected bonds or contacts, keep blank in the corresponding control in the dialog window. For example, if you have selected nine bonds with the interior color red and one with yellow, the color selection field for the interior color will be empty. If you leave this field empty, the interior colors of the selected objects will be untouched. If you select a color, all selected bonds will get that new interior color.

Thin vs. Thick Bonds

While there are a lot of styles with different ORTEP-like patterns for atoms, bonds can have two different styles only: Thin and thick. Besides this, you can further assign the style "invisible".

Thin bonds are displayed as lines only. These lines can have a dotted style instead of the default solid line style and a defined thickness in millimeters to enhance them in the structure picture. In rendered representation, these thin bonds are also represented as lines only instead of 3D objects (cylinders), and will thus not be shaded.

Thick bonds are displayed as 3D objects, that means as cylinder, which may be distorted due to perspective transformation or a 3D effect, called bond tapering. In extereme cases these cylinders become cones. The radius of the bond is given in Angstroems units. In rendered representation, thick bonds are displayed as 3D objects and can be shaded like atoms.

Design and relative length of broken-off bonds

Both Bond Design and Bond Group Designs dialog have a second page beneath the Style and Colors page. On the Others page global settings that apply to bonds of all bond groups can be adjusted. In the current Diamond version there is only the relative length to be used for broken-off bonds. Broken-off bonds are bonds between atoms at the borders of the structural model and their invisible hypothetical neighbours just outside the model. These bonds are generally shorter than they normally would be; you can adjust their length by modifying this factor. This factor is given in the input field Relative length of broken-off bonds.

Note that this factor is a global value used for all broken-off bonds in a structure picture. It cannot be varied individually like colors or styles of individual bonds.

The basic design of broken-off bonds can be defined on the Style and Colors page of the Bond Group Designs dialog by selecting the item "Broken-off bonds" in the tree list of connection types and bond groups. Like regular bonds, you can change colors, styles, and fragmentation later individually for broken-off bonds - but the relative length is the same factor for all broken-off bonds within a structure picture.

Fragmentated Bonds

If you cut a bond into pieces each with the same length and with voids between having the same size, you get what Diamond (and at least SCHAKAL) calls a "fragmentated" bond. Fragmentation can be applied to both thin and thick bonds.

To define a bond as fragmentated and define the number of voids between the fragments, choose the Bond and Contact Designs command from the Display menu, and select the Style and Colors page of the dialog. (This may be the Bond Group Designs or Bond and Contact Designs dialog depending on the situation.) Edit the number of voids in the input field Fragmentation. A number of zero defines a "normal" bond without fragmentation.

Several bond styles in flat (left) and rendered (right) representation: Thin bonds (in the rear), thick bonds with a radius of 0.04 Angstroems appearing as tapers (bond tapering factor of 0.8) (in the front), a thin fragmentated bond (going to the bottom atom), and a thick fragmentated bond (going to the top atom), both with a fragmentation of 4.

Colors and Styles

The design of a bond or bond group or any other connection type (e.g. contact) is made up of the following settings:

Since rendered representation uses no edges, the settings edge color, pen, and thickness will be used only in flat representation.

You will find all these settings on the Style and Colors page of the Bond Design dialog or Bond Group Designs dialog, rsp.

Interior color and brush; Edge color, pen, and thickness

Interior color and brush as well as edge color, pen, and thickness of a thick bond works in principal like for atoms, so please compare with "Colors and Styles". For a thin bond (or contact), the interior color is used to define the line color, whereas the line style (solid, dotted, etc.) and thickness are defined by the edge pen and thickness.

Rendered representation

When using rendered representation, bonds/contacts use the interior color only. No edge is used.

Using the mouse wheel to change bond radii

Diamond offers several so-called "mouse wheel modes". These modes have in common that a tick of the mouse wheel changes a property each. (To get more informations about the several mouse wheel modes, read the article "Using the Mouse Wheel".)

Here we show the wheel mode to scale radii of (thick) bonds and contacts. It either applies
- to the selected bonds or contacts only, if at least one bond or contact is selected, or
- to all bonds, if no bond or contact is selected.

Every tick of the mouse wheel increases the radius of the (selected) bonds/contacts by some percent. The starting point is 100 percent (or "1x"). To enlarge the bond/contact radius/radii, move the mouse wheel forward. To reduce the radius/radii, move the mouse wheel backward. The maximum value is reached, when the radius corresponds with the radius of the connected atoms, whereas when the minimum value (radius zero), the representation turns to thin (wire) bond/contact each.

To start the wheel mode "bond radii" either:
a) click with the mouse wheel button into (one of) the selected bond(s)/contact(s) in order to apply the radius variation to selected bonds/contacts only. (A bond or contact will be selected, if it is not yet selected.) Or click outside any bond/contact, if you want to apply the bond/contact radius variation to all bonds/contacts in the structure picture. (Any selection will get lost, if you click outside, unless you hold down the Ctrl or Shift key.) This will poup the mouse wheel control window with the latest used wheel mode. Change to "Bond Radii", if necessary, by clicking on the corresponding button (highlighted in the image below).
b) Or run the command Bond Radii from the Tools -> Mouse Wheel Action sub-menu.
The blue blinking square(s) indicate(s) which bond(s) and contact(s) will be changed. (There are no blinking squares, if the changes will affect all bonds and contacts.)

Alternatively, you can do a long click with the mouse wheel button, which selects the whole molecule. (The blue markers now frame the whole molecule.)

The histogram in the control window shows the scaling factor relative to the starting point of the mouse wheel mode ("1x", "2x", etc.).

Since no bond has been selected in our sample structure picture, the "Bond Radii" mouse wheel mode refers to all bonds in the structure picture. (There are no contacts in the picture.) When starting the wheel mode, the blue ruler is on the "1x" position. The (absolute) radii of the bonds are given in the top right of the histogram, here all bonds have the default radius for thick bonds: 0.05 Å.

Scale the bond radii factor relative to the radii when the mouse wheel action has started (100 percent or 1x) by turning the mouse wheel up and down.

You can click on the Restore button (below the histogram) to reset the bond/contact radii to the original sizes they had when you started the bond radii mouse wheel mode.

The pin button at the right end of the upper icon row changes between permanent and temporary display of the control window. To re-display the control window after it has disappeared after a short while, press the F7 key. The small red/white 'x' in the right end of the title bar of the control window hides the window.

To terminate the bond radii mouse wheel mode, either simply press the Escape key, or click on the closing button of the mouse wheel control window (the left-most in the upper icon row: the 'x' symbol.

Material Properties

A bond uses the same material properties as an atom, as far as it has been defined as thick bond, and rendered representation has been enabled. Then it is drawn as a real 3D object (a cylinder that may be distorted to a taper) and thus can be shaded. If it has been defined as thin bond only, it will be drawn as a simple line instead without shading effects.

For the different material properties, see the section "Material Properties" in the article "Designing atoms".

Assigning Selected Properties to Multiple or All Connection Types

Suppose all your bond types use thin green bonds, and now you want to assign all bond types thick yellow bonds with black edge, you could - one bond type after the other - select the bond type, change style and colors, then select the next bond type, change style and colors, etc.

To avoid this, the connection type and bond group tree list offers multiple selection. So simply select all bond groups and/or connection types in the tree list, then set the properties in the Colors and Styles page.

Copying and Pasting Bond Styles

Like for atoms, Diamond offers a powerful and easy to use way to assign a style to one or more selected bonds (or contacts or H-bonds):

1. With the right mouse button, click on the bond whose style (colors, edge, radius, fragmentation, material properties) you want to assign to other bonds, and choose the Copy Style command from the context menu.

2. Select the bond or multiple bonds (or contacts and/or H-bonds) you want to assign that design to. With the right mouse button, click into one of the selected bonds, and choose the Paste Style command from the context menu.

Please note that for the Copy Style command more than just one bond (or contact or H-bond) can be selected. If these multiple bonds etc. have deviating design properties, e.g. seven grey and one blue bond, this property (here: the bond color) will be set to "indeterminate", and the bonds this design will be pasted to will not change this indeterminate property, that means the bond color will remain unchanged.

Previous article: Designing atoms
Next article: Drawing ellipsoids

References:
ICSD:23119: Jackson P F, Johnson B F G, Lewis J, Nicholls J N, McPartlin M, Nelson W J H; "Synthesis of the Carbido Anion (Os₅ C (C O)₁₅ I)and the X-Ray Crystal Structures of Os₅ C (C O)₁₅ and Ph₃ P)₂ N) (Os₅ C (C O)₁₅ I)"; Journal of the Chemical Society, Chemical Communications (1972-), 1980, 564-566 (1980).
COD:1501635: Ulrich Darbost, Janie Cabana, Eric Demers, Thierry Maris, James D. Wuest; Molecular Tectonics. "Use of Br...aryl Supramolecular Interactions for the construction of Organized Networks from 9,9'-spirobifluorene in the Crystalline State"; CheM, 1 (2011), 52-12369.
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).
COD:7103386: Rang, Alexander; Nieger, Martin; Engeser, Marianne; Lützen, Arne; Schalley, Christoph A; "Self-assembling squares with amino acid-decorated bipyridines: heterochiral self-sorting of dynamically interconverting diastereomers."; Chemical communications (Cambridge, England), *, 4789-4791 (2008).