Diamond Version 5 User Manual: Exploring bonding and contact spheres

Working in Exploration View

This article describes how to work in Exploration view, especially in contrast to the regular Picture Edit view:
- The Exploration Controller
- Creating a single atom or molecule or cell content
- Choosing a target to study
- Rotating, shifting, and scaling your picture
- Growing or shrinking spheres around atoms
- Completing molecular fragments or cutting back molecules
- Removing atoms and bonds
- Taking or copying an image of the picture
- Closing Exploration view

Previous article: Overview
Next article: Exploring bonding spheres

The Exploration Controller

The Exploration Controller docking window consists of four parts: The selection of what to inspect, a distances histogram, a distances table, and buttons to choose settings as well as actions, e.g. build or complete a molecule in the graphics view.

What to explore
- Bonding spheres, that means strong interactions. These are stored in the Connectivity (on atom type/group level) and the Atomic Environments (atom site level).
- Contact spheres (non-bonding interactions) as well as H-bonds. These are also stored with the connectivity on atom type or on atom site level.

Apply to
- Atom: This is the typical application, to study the (bonding or contact) sphere around a selected atom (reference atom).
- Bond: This checks only the bonding sphere of the reference bond or the contact sphere, if the reference is a contact not a bond.
- Molecule: This is similar to the application Atom but refers to all atoms of the molecule (or molecular or polymeric fragment) where the currently selected atom(s) belong to. This is useful, if you want to study all contacts/H-bonds from this molecule to other molecules (as well as intermolecular contacts/H-bonds).
- All: This refers to all atoms that are part of the structure picture in the graphics view. It is recommended or only reasonable to choose an atom type/group pair (bond group), e.g. to study the distances between C--O only.

Central atom or Bond
The dropdown list offers the commands:
- Add atom as target, which calls the Add Atom dialog to choose an atom from the atomic parameter list to be added to the structure picture and to serve as reference atom for the study of bonding or contact spheres. The list in the dialog contains only atoms that are not yet available in the structure picture. It is empty, if at least one (symmetry-equivalent) atom of the parameter list is part of the structure picture.
- Choose target, which calls the Choose Target dialog to choose an (already existing) atom or bond (or contact) from the structure picture. Please find details below at "Choosing a target to study".
Besides this, the dropdown list stores the latest visited or studied atoms and bonds.
Note: If you choose a bond rather than an atom as target, the label "Central atom" changes to "Bond".

Atom group pair
Usually this is set to (All) which means there are no restrictions concerning the atom group (atom type) pairs you are studying. The dropdown list contains a list of all atom types. It is useful or reasonable to choose a bond group, i.e. atom type/group pair when you apply your study to all atoms or all atoms of a molecule.

Screenshot of Exploration Controller when studying the contact sphere around the atom "O2" in [...] Contact sphere is purple, the bonding sphere in contrast is yellow.

The distances histogram and the table of neighbouring atoms depend on what is explored: bonding or contact spheres. These are described in more details in the following two articles "Exploring bonding spheres" and "Exploring H-bonds and contact spheres".

The Settings button is still provisional in the current Diamond version. The Actions button opens a menu with several commands for building up the structural framework in the graphics view as wells as how to view and some additional helper functions. These are explained in more details below.

The Close button ends the exploration view and returns to the regular Picture Edit view (or to the Thumbnails Preview, if you launched the exploration from there).

Creating a single atom or molecule or cell content

Regardless if you study bonding or contact spheres, there are several options where to start your studies from:
- Creating a single atom of the parameter list and check the sphere around.
- Creating a molecule and checking contacts and/or H-bonds to neighbouring molecules.
- Filling the content of the unit cell.

The corresponding commands are available from the context menu of the graphics part (screenshot below) and from the Actions menu of the Exploration controller (screenshot above).

Context menu when there are no atoms yet in the structure picture. The three basic commands to generate atoms and bonds are at the top of the menu.

Add Atom(s)
This command is suitable to add a first atom to an empty structure picture to study its environments, especially in inorganic or metal-organic compounds. The Add Atoms dialog offers a list of atom sites where you can choose one site (or more or all sites) from.
- In the case of an empty picture all atoms of the atomic parameter list are listed at their original x/a, y/b, z/c positions.
- If there are already atoms in the picture, the atoms not yet present in the picture are listed in the dialog only. Depending on the positions of the present atoms, the list may include symmetry-equivalent positions.
- If there is an atom under the mouse cursor and/or a reference atom already defined, an enclosure sphere is given and the atoms that are not yet present in that sphere are listed. You can change the radius of the enclosure sphere in the dialog.

Get Molecules
This command creates a molecule automatically from scratch based on the atomic parameter list. This molecule is a good starting point to study contacts and H-bonds to neighbouring molecules (also amongst intramolecular contacts). Depending on the structure parameters there may be multiple molecules defined in the atomic parameter list and/or polymers, eventually plus vagabonding atoms.

Fill Unit Cell
This command fills the contents of the unit cell. All atoms within the unit cell plus/minus a tolerance parameter epsilon will be created in the structure picture. Fill Unit Cell is suitable to get a quick overlook in a bigger moiety in an inorganic polymeric framework or to study a packing of molecules after running a Complete Fragments command, see below.

Note: These basic building functions are a small subset of possible functions in Diamond to build up a structure picture manually. These are available in the regular Picture Edit view and are described in detail in the chapter Building up structural parts of this manual.

Choosing a target to study

If your structure picture that you use for the exploration already has atoms, you can choose the atom (or bond or contact), whose bonding or contact sphere you want to study, in the Exploration Controller (as mentioned above) or from the context menu of the graphics view.

If an atom or a bond or contact is already marked as selected in the Picture Edit view, this will automatically be chosen as target when you enter the Exploration view. If you go through the Start Exploration dialog (see the previous article "Overview"), the object is selected in the dialog but you can choose a different one.

Screenshot of the "Start Exploration" dialog when atom "N1" has been selected in the Picture Edit view. The dropdown list offers all atom sites of the parameter list and shows you how many atoms are already in the structure picture and how many and which are selected, if any.

Regardless, if you come directly to the Exploration view through toolbar button or acceleration key of from the Start Exploration dialog, the selected atom or bond, rsp. is given in the Exploration Controller under Central atom and Bond, rsp. Apply to gives you the option to choose the whole molecule, which the reference atom or bond is part of, so you can see all contacts/H-bonds of a molecule. If you study bonding spheres rather than contact spheres, it may be reasonable to make a restriction under Atom group pair.

  
Screenshot of controller when the atom "N1" is pre-selected (left) and when the bond C1--N1 is pre-selected (right). A pre-selection of a bond automatically chooses the corresponding atom group pair, here: N--C.

You can choose an atom or bond (or contact) that you have chosen as target before or "visited" before, even if you left the Exploration view in between and have returned later. "Visit" means that you move the mouse cursor over an atom or bond (or contact) and Diamond shows you infos about the object under the mouse cursor, such as atom label (or labels of the connected atoms, rsp.), the atomic coordinates (or interatomic distance, rsp.) and composition of the current atomic environment.

The dropdown list at "Central atom" gives you quick access to the recently visited atoms and/or bonds. Besides this you can choose another target through the Choose Target dialog, which is described below, or add an atom as target that is not yet in the picture.

The context menu of the graphics view offers the options of the Exploration controller at the top (below "Explore what" where you decide between bonding and contact spheres) in the Apply to sub-menu:
- Atom, Bond, Molecule [at...], and All atoms.
- Choose Target... calls a dialog and is described below.
- Clear Target detaches the reference atom or bond, rsp., with the result that no target is selected, just like you have entered the exploration with no selections in the structure picture.

  
Upper part of the context menu of the graphics view when there is no atom or bond pre-selected (left) and with a pre-selected atom, here: "N1" as reference atom (right).

Choose Target dialog
Here you can choose the reference atom and if to apply to the reference atom/bond/contact only or to the molecule or to all atoms of the structure picture and make a limitation to the atom group pairs whose bonding or contact spheres are to be checked.
- Choose an atom/Choose a bond as reference: This is to switch the list Reference atom or bond, rsp. between all atoms present in the structure picture and all bonds (or contacts or H-bonds), rsp. to choose the reference object.
- The Target options specify, (a) if to study only the bonding/contact sphere around the reference atom or only the bonding/contact sphere specified by the reference bond or contact) or (b) to study all bonding/contact spheres of the molecule belonging to the reference atom or reference bond, rsp., or (c) all bonding/contact spheres of the whole structure picture.
- The Consider options are to make a limitation to bonds or contacts matching only a pair of atom groups or not. With Consider only bonds/contacts belonging to atom group pair only bonds or contacts will be considered that match the pair of atom groups that is selected in the dropdown box right beneath.

Atom group pair
This option is available as combobox in the Exploration controller, as sub-menu in the context menu, and the "Choose Target" dialog shown above. If an atom group pair (i. e. usually a pair of elements optionally with oxidation numbers) is selected, bonding or contact spheres will be only considered when they belong to the selected atom group pair or neighbouring atoms are considered only if it (together with the reference atom) matches this atom group pair.
- All removes a limitation (if defined) to a certain pair of atom groups where bonding or contact spheres are checked. That means all atoms of the molecule or the whole structure picture (depending on the Apply To [...] setting) will be considered again.
- Choose Atom Group Pair... calls the corresponding dialog where you can choose an atom group pair.
- In the Exploration controller you can choose an atom group pair directly from the dropdown list, which lists all pairs of atom groups available in the current structure.

Rotating, shifting, and scaling your picture

Rotating, shifting, and enlarging/decreasing with the mouse is handled like in Grab mode, which is known from the Picture Edit view. (The original Grab mode offers more options, see the article "Grab mode".)

Rotating the structure
Rotation is done by moving the mouse cursor while the left mouse button is down. The rotation mode uses arcball rotation: You rotate a virtual point under the mouse cursor position or an object (atom or bond) at the current mouse position across a hemisphere. This mode rotates about all three axes x, y, z of the viewing coordinate system.

Shifting the structure
Pressing down the right mouse button initiates shifting mode. The structure picture follows the mouse position horizontally and vertically unless the right mouse button is released.

Changing the enlargment factor
Turning the mouse wheel with no status key (Shift, Ctrl) pressed changes the enlargement factor, i.e. "zooms" in or out. While the enlargement factor changes, the atom under the mouse cursor keeps its 2D position in the graphics view.

Commands to set or change the center of rotation

These are available through the Rotation Center sub-menu of the graphics view's context menu or the Exploration controller's Actions menu:

About automatic centering
Like the Picture Edit view, the Exploration view has an automatic centering option, which sets the center of rotation automatically to the mean values of all atoms' coordinates after an operation that adds or removes atoms to or from a picture. The Exploration view takes the automatic centering option from the Picture Edit view. Since the automatic centering is active by default in Picture Edit view, it is also active by default in the Exploration view.

You may find it disturbing - in Exploration view more than in Picture Edit view - when there is an incomplete molecular or polymeric fragment and the structure slips to the side when you add atoms, e.g. when filling incomplete coordination spheres or completing the fragment to a molecule. Then you can or should disable the automatic centering by clearing the checkmark in the Automatic Centering command. The options for automatic centering are treated separately for Picture Edit view and Exploration view.

Putting the rotation center into an atom
If the mouse cursor is over an atom, the command Put Rotation Center puts the center of rotation into the atom's position. If there is no atom under the mouse cursor but a reference atom is defined, Diamond takes the reference atom's position instead. The command is grayed (i.e. not available), if neither an atom (or bond) is under the mouse cursor nor a reference object defined.

The command also works for bonds and contacts. In this case the coordinates of the center of the bond/contact are taken.

Resetting the rotation center
The Reset Rotation Center command puts the center of rotation into the center of all atoms that are currently in the picture, i.e. the rotational center's coordinates x,y,z are the mean values of all atoms' coordinates.

Commands in the Picture Viewing sub-menu of the context menu

The Picture Viewing sub-menu of the graphics view's context menu or the Exploration controller's Actions menu contains commands dealing with viewing directions and picture adjustment:

Viewing along an axis
The three commands Viewing along a-, b-, or c-axis change the orientation of the structure picture in this way that the vector a, b, or c, rsp., of the unit cell point towards you.

Adjusting
The two commands Adjust Position and Adjust All both adjust the structure within the 2D drawing area by shifting the 2D position (of the 3D rotational center). While Adjust All also adjusts the enlargement factor (cm per Angstroem) and the camera position to fit the structure picture in the drawing area., Adjust Position does not, even if some objects of the structure picture are still not yet visible.

Enlarging or decreasing at a certain atom's position
The two commands Enlarge Here and Decrease Here increase and reduce, rsp., the enlargement factor (cm per Angstroem) but keep the clicked position (i.e. the atom or bond under the mouse cursor) within the 2D drawing area.

Moving the clicked position into the center
The two commands Enlarge and Center and Center Here move the clicked position into the 2D center of the drawing area. While the enlargement factor remains unchanged with Center Here, the command Enlarge and Center increases the enlargement factor.

Rotating and object to the front
The command Rotate Here rotates the "clicked position" to the front. This position may be an atom or a bond or a virtual 3D point on the front hemisphere of the arcball (see above) that surrounds the structure picture. Finally the atom (or bond or virtual point) becomes the frontmost point lying on the +z-axis (pointing towards the viewer) of the viewing coordinate system.

Note: This article touches only a part of structure picture viewing options in Diamond. More details (but referring to regular Picture Edit view) are available from the articles Projection and Orientation and Position.

Growing or shrinking spheres around atoms

Provided that are already atoms in the structure picture, the context menu of the graphics view offers additional commands to add (or remove) atoms regarding the current bonding conditions. (In the Exploration controller's "Action" menu these commands are disabled (grayed) when there are no atoms yet.)

The Fill All Bonding Spheres command completes all bonding spheres around all atoms of the current structure picture. This means, every atom of the structure picture is checked, if all of its bonding neighbouring atoms are present. Missing neighbouring atoms are added, if necessary. This command runs only one cycle, which means that it does not necessarily complete an incomplete fragment to a molecule - as the below mentioned "Complete fragments" functions do.

The command Grow Spheres at "(atom label)" "grows", which means completes, the bonding sphere around the atom under the mouse cursor, if the context menu has been called for a clicked atom. It "grows" the sphere of the reference atom, if a reference atom is defined but no atom under the mouse cursor. This "growing" is also know as "pumping up", since it checks subsequent spheres, if the current enclosure sphere is already complete - up to the outmost bonding sphere. This works even if there are already one or more completed coordination spheres around the actual central atom.

In contrast to "Grow Spheres", the command Grow Fragment at "(atom label)" regards the whole fragment where the atom "(atom label)" belongs to. It can be used to grow a polymeric part of a structure or an (already) incomplete molecular fragment. "Grow Fragment" performs only one cycle, i.e. completes only the farmost incomplete bonding spheres, but this does not necessarily yield to a complete molecule.

The command Shrink Spheres at "(atom label)" works the opposite way as Grow (Pump up) Spheres. It "shrinks" a bonding sphere, i.e. removes the atoms from the farmost bonding sphere of the atom "(atom label)".

Completing molecular fragments or cutting back molecules

The Complete All Fragments command completes all fragments in the structure picture to complete molecules, if possible. If at least parts of the structure are polymeric, it stops the operation after several cycles.

The command Complete Fragment at "(atom label)" completes only the fragment where the atom under the mouse cursor or the reference atom belongs to rather than all fragments.

The command Cut Back Fragment at "(atom label)" works the opposite way as "Grow Fragment" (see above). Here Diamond looks for the outmost atoms of a polymer or molecule (or molecular fragment) and destroys them.

Removing atoms and bonds

The Destroy commands from the context menu and from the Actions menu can be used to get rid of one or more atoms or of whole fragments, molecules or even the whole content of the structure picture.

To remove the atom under the mouse cursor, run the command Destroy Atom at [...]. The atom is removed together with associated bonds, contacts, and H-bonds. The command is also available, when there is no atom under the mouse cursor but a reference atom is defined. In that case, the command removes the reference atom, with the consequence that no target is defined after.

The related command Destroy Bond at [...] removes the bond mentioned after "at" or similar objects like a contact or H-bond but not the connected atoms themselves.

The command Destroy Molecule/Fragment at [...] removes the whole molecule where the atom or bond mentioned after "at" belongs to. This can also be an incomplete molecular or polymeric fragment.

Finally, the command Destroy All removes the complete contents of the active structure picture, i.e. all atoms, bonds, contacts, and H-bonds.

Taking or copying an image of the picture

You can use the command Take Picture (context menu or Actions menu) to create a new structure picture object as a complete copy of the current picture. (While the new picture is dropped, you will continue working with the current picture in the Exploration View.)

The dropped picture may be used later (after returning from the exploration) for publishing or as a starting point for later exploration and improvements. (Or simply delete it when it is not more of interest.)

You can let Diamond "take" a picture automatically immediately before the exploration view begins, if you launch the exploration through the Start Exploration command in the Picture menu and set the checkmark at Take a copy of the picture before exploration begins in the Start Exploration dialog.

If you have launched the exploration through the Start Exploration command of the Picture main menu and the setting Take a copy of the picture before exploration ends was activated in the Start Exploration dialog, a copy of the picture with the designs of the exploration will be dropped ("taken") automatically before the designs are restored (if the Backup and Restore option was activated).

(Note: More options to take a picture are available in the Picture Edit View: See the article "Deriving new pictures".)

Copying an image
To get a 2D image - rather than a copy of the 3D Diamond structure picture - use the Copy Graphics command. It copies the contents of the current structure picture graphics as 2D bitmap data to the Windows clipboard, so that it can be pasted (as "bitmap" or "device-independent bitmap") by other applications.]
This is described in the article "Copying the Contents of the Structure Picture".

Closing Exploration view

The picture exploration view can be closed with:
- the Close button in the Exploration controller or
- with the Close Exploration command in the context menu of the graphics view.

Both the Close Exploration command and the Close button terminate the current exploration (of bonding or contact/H-bond spheres) and return to the (regular) Picture Edit view, if you started the exploration from the Picture Edit view, and to the Thumbnails Preview, if you started from there.

Since the atom and bond design of the structure picture has been backed up when entering the exploration view, this design will be restored when you leave the exploration. Note: The design is not restored, if you have launched the exploration through the Start Exploration command of the Picture main menu and have cleared the checkmark at Backup and restore picture design in the Start Exploration dialog. (Backup and restore of design is activated by default in the dialog. When you use the toolbar button or the acceleration key, the design is backupped and restored anyway.)

You can make a restore of design undone using the Undo command from the Edit menu when you have returned from Exploration view, if you want to keep the design changes that the exploration view applied to the structure picture.

Screenshot of the dropdown list at the Undo button to make a previous Restore Picture Design undone. If you click on "Undo (1) Restore Picture Design (End Exploration)", your changes done during the exploration leave unchanged and the design shown during the exploration is restored. If you click on "Undo (2) Begin Exploration", all changes made in the exploration will be discarded.

Previous article: Overview
Next article: Exploring bonding spheres

References:
COD:7106313 - Zhongxuan Xu, Kun Huang, Tong Liu, Mingjin Xie, Hongbin Zhang: Synthesis of spirocyclic ?-keto-lactams: copper catalyzed process. Chem.Commun., 47, 4923 (2011).