Diamond Version 5 User Manual: Modes of operation

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

This article is about:
- Tables overview
- Contents and settings
- Table of atomic parameters
- Table of bond parameters, table of H-bond parameters, and table of contact parameters
- Table of created molecules (or fragments)
- Selecting Atoms, Bonds, or Polyhedra From an Object List
- "Select in Table" command
- Selecting atoms, bonds, or contacts from tables

Previous article: Selecting objects
Next article: "Atom list": Hierarchical list of atom groups, atom sites, and created atoms of a structure picture

Tables Overview

The secondary pane (or data pane) of the structure picture window can be used to display several object lists:
- the atomic parameter list including anisotropic displacement parameters,
- lists of connection parameters: bond parameters, H-bond parameters, and contact parameters,
- the table of created atoms,
- the table of created bonds.

Besides the tables for atomic and connection parameters and created atoms and bonds, there are also tables for atom groups and bond groups. By default an atom group combines all atoms of the parameter list belonging to the same atom type. A bond group is a combination of two atom groups each. Cf. the article "About atoms, atom groups, bonds, and bond groups".

The table of polyhedra lists all coordination polyhedra and Voronoi polyhedra currently present in the structure picture and is described in the article "Polyhedron selection and properties".

The table of created molecules lists all molecules present in the current structure picture, if at least one of its constituent atoms is present in the structure picture. Given is the formula sum of molecule and fragment as well as the label and symmetry of the reference position.

There are also tables for reported distances, angles, and torsion angles, which may come from measuring distances, angles, or torsion angles, rsp., as well as tables for H-bond infos (typically from imported CIF H-bond loops). These are described in the article "Measuring and reporting distances, angles, and torsion angles".

The table of extended geometric infos is described in the article "Extended geometric infos: Angles between planes etc.".

To open an object list, choose the Table command from the View menu, and select the corresponding entry from the submenu. If the data pane has not yet been opened, Diamond switches to split mode, where you can define the width of the object list.

For each object list, you can select the columns to be displayed as well as the sort criterion.

More informations about the object that is selected in the table can be shown in the "Properties view", which is by default placed below the table in the data pane.

The object lists can be used as versatile aid to select atoms, bonds, or polyhedra in the structure picture.

Contents and Settings

To change the format of a table (object list), choose the Table Settings command, which is available from the main menu (View -> Table -> Table Settings) or from the caption bar of the table (see screenshot) or from the context menu of the table:

To adjust column widths, use the mouse to drag the separators to the left or right. To change the sort order, click on the corresponding header of the column. To invert the sort order, click once again on the header.

The column to be sorted (and the sort direction ascending or descending) can also be set in the Data Table Settings dialog, opened from the Table Settings command. The list in the dialog shows all columns that are available for the current table.

Table of atomic parameters

The table of atomic parameters may contain the following informations about each atom in the atomic parameter list including its anisotropic displacement parameters:

Screenshot of the table of atomic parameters and properties of the atom "As1" that is selected in the table.

For more details read the articles "Atomic parameters" and "Support for disorder parts".

Tables for bond, H-bond, and contact parameters

Since version 4 Diamond supports explicitely defined bonds (i.e. strong or "regular" bonds), H-bond definitions, as well as non-bonding contact definitions. These are the bond, H-bond, and contact parameters, rsp. Usually they come from "_geom_bond_xxx" etc. loops in CIF structure data files. In analogy to the atomic parameters, you can define/edit them through the command Connection Parameters in the Structure menu. More details are in the article "Connection parameters".

Like for the atomic parameter list, the parameter list tables for bonds, H-bonds, and contacts can be shown through the sub-menu Table in the View menu, or simply through a drop-down menu from the main toolbar:

Table of bond parameters
The default setting of the bond parameters table shows (taken with sample file "COD-1500005.cif"):
- sequential number in bond parameter list,
- type (not supported in this beta version yet),
- Label and symmetry of the first atom (typically "x, y, z"),,
- label and symmetry of the second atom,
- distance in Angstroem between atom 1 and atom 2.
To add or remove columns, run the command "Table Settings..." from the above mentioned menu (or "View" -> "Table" -> "Table Settings...").

The properties pane below the bond parameter table gives somewhat more details about the highlighted bond. (To open the properties pane, run View -> Properties, and shift the divider between table and properties pane, if necessary.)

Table of H-bond parameters
The default setting shows columns for (same sample COD:1500005):
- sequential number in H-bond parameter list,
- type (not supported in this beta version yet),
- labels of: donor atom, H-atom, and acceptor atom,
- distances in Angstroem between donor and H, H and acceptor, and between donor and acceptor,
- distance in Angstroem between donor and acceptor relative to van der Waals radii sum of donor and acceptor,
- angle, in degrees, between donor, H, and acceptor.

Table of contact parameters
To complete the connection parameter table survey, the columns of the table of contact parameters show (here no example):
- sequential number in contact parameter list,
- type (not supported in this beta version yet),
- Label and symmetry of the first atom (typically "x, y, z"),,
- label and symmetry of the second atom,
- distance in Angstroem between atom 1 and atom 2.
- distance in Angstroem between atom 1 and atom 2 but relative to the two atoms' van der Waals radii sum.

Table of created atoms (and atom-like objects)

The table of created atoms contains a list of all atoms that are currently present in the structure picture, along with informations about their "source atom" in the atomic parameter list, the symmetry operation applied, and the coordinates and some more optional columns. Besides this, also pseudo-atom objects (e.g. cell corners) are listed in the table.

The following columns are available:
- The sequential number of the (created) atom in the list of created atoms. (Note that numbers 1 through 4 are reserved for the origin of the coordinate system, and the three endpoints of the three crystallographic axes a, b, c of the unit cell.)
- The atom site symbol. This is the label of the atom in the atomic parameter list. If the site is occupied by multiple atoms, all labels are given.
- The symmetry operation indicating, if and how the atom has been created from the atom in the parameter list.
- The atom code, which indicates the number in the atomic parameter list and the symmetry as well as integer cell translations in a numeric code.
- The extended atom site info, which is just the atom label for a single full site but a composition of multiple atoms along with their site occupations, if occupied by multiple atoms of the parameter list.
- The crystal coordinates x/a, y/b, z/c of the atom in the structure picture (which is only identical with the coordinates in the atomic parameter list, if it has been created with the trivial symmetry operation "x, y, z").
- The orthogonal coordinates x, y, z in Angstroem units.
- The view coordinates x, y, z in Angstroem units (which deviate from the orthogonal coordinates, if the default viewing is not used where the a-axis points to the right, the b-axis to the top and the c-axis to the user).
- The number of bonds presently connected to the atom in the structure picture (which is not necessarily identical with the number of neighbouring atoms in the atomic environment).
- The disorder part where the atom belongs to, if disorder is defined in the atomic parameters.

Table of bonds (and contacts, H-bonds or other bond-like objects)

The "table of bonds etc." contains a list of all bonds as well as H-bonds and non-bonding contacts that are currently present in the structure picture, along with their connected "source atoms" in the atomic parameter list, the corresponding atom codes, and the bond length. Besides this, also pseudo-bond objects like cell edges are listed in the table.

The following columns are available (but not all displayed by default):
- The sequential number of the (created) bond (or contact or H-bond or cell edge) in the list of created bonds.
- The type, e.g. "reg." for a bond, or "cnt." for a non-bonding contact, or "<CELL>" for a cell edge pseudo-bond.
- The symbol (label) (or symbols if the site is occupied by multiple atoms) of atom #1.
- The symmetry operation indicating, if and how atom #1 has been created from the atom in the parameter list.
- The atom code of atom #1, which indicates the number in the atomic parameter list and the symmetry as well as integer cell translations in a numeric code.
- The extended atom site info of atom #1, which is just the atom label for a single full site but a composition of multiple atoms along with their site occupations, if occupied by multiple atoms of the parameter list.
- The crystal coordinates x/a, y/b, z/c of atom #1 in the structure picture (which is only identical with the coordinates in the atomic parameter list, if it has been created with the trivial symmetry operation "x, y, z").
- The symbol(s)/label(s) of atom #2.
- The symmetry operation applied to create atom #2 from the corresponding atom of the parameter list.
- The atom code of atom #2.
- The extended atom site info of atom #2.
- The crystal coordinates of atom #2.
- The bond length (or in general distance between atoms #1 and #2), in Angstroem.
- The disorder part, if given, where atom #1 and atom #2 belong to.

Table of created molecules

The table of created atoms and table of created bonds are now accompanied by the table of created molecules. Like the first two mentioned commands, you find the command to show the table of created molecules in the "Table" sub-menu of the "View" menu. You may access the table quicker via the toolbar (right part, see screen shot at the top).

In the table of created molecules every molecule of the current structure picture is listed -- whether it is complete or just fragmentated -- or just one or two atoms of the molecules have yet been created.

The following picture is from sample file "COD-1500005.diamdoc" and shows a unit cell packing with the option to cut molecules at the boundaries. So the table of molecules contains both complete molecules and fragments.

The default settings show:
- the sequential number of the molecule in the structure picture,
- the title of the molecule from the list of molecular units. (See how molecular units are defined: "Build" -> "Molecules" -> "Define")
- the formula sum of the entire molecule, as it is defined from the molecular unit list,
- the formula sum of the molecule, if complete, or (in brackets) the fragment, if incomplete,
- the numbers of present atoms and total number of atoms of the molecular unit,,
- the numbers of present bonds and total number of bonds of the molecular unit,
- the reference atom of the molecular unit,
- the crystal coordinates (x/a, y/b, z/c) of the reference atom.

In the sample, "Molecule 6" with reference atom "Co3" at (x, 1/2-y, 1/2+z) is complete, as well as "Molecule 7" at (x, y, z) is, but other symmetry-equivalent molecules of "Molecule 6" are incomplete (only 17 of 25 atoms and 16 of 24 bonds).

The properties pane shows more details about the highlighted molecule in the table, especially the list of constituent atoms and bonds with their crystal coordinates.

Selecting Atoms, Bonds, or Polyhedra From an Object List

The object lists in the secondary pane of the structure picture window support the selection of atoms, bonds, and coordination polyhedra in the structure picture. Both the list of created atoms and the list of created bonds represent the created atoms and bonds, rsp., of the structure picture in the graphics pane. Thus if you select an atom (or multiple atoms) in the graphics pane, it will automatically be selected in the atom list, and vice versa. The same is for bonds in the graphics pane and in the bond list. Of course, you can combine selection in the graphics pane with selection in the object list. For example, sort the atoms in the list for atom symbols, then select a range of rows, and finally change some selection in the graphics pane by using extended selection. (Hold down the Shift key and click with the left mouse button to invert the selections of several objects.)

The lists of atomic parameters, atom groups, and bond groups may assist you when selecting atoms or bonds, rsp., which are associated with selected atoms from the parameter list or atom groups or bond groups. If you want to select all atoms in the structure picture, which are derived from - for example - the atom with the symbol "P(1)", open the table of atomic parameters and select the atom "P(1)" in this list. Then choose the Select atoms command from the context menu of the list, which will select all atoms in the graphics pane that are derived from "P(1)". In principle, you can use the same method for the lists of atom groups and bond groups. From the bond group list, you can select all created bonds associated with the selected bond groups.

If you use the table of coordination polyhedra, the central atoms of the selected polyhedra will automatically be selected in the graphics pane, and vice versa.

"Select in Table" command

The Select in Table command from the Edit menu enables you to select an item (or multiple items) in the table in the right pane of the Diamond document window basing upon the currently selected objects in the structure picture.

While selection between atoms and bonds in the structure picture is automatically synchronized with the table of created atoms and the table of created bonds, rsp., other tables do not automatically synchronize their selections with the selections in the structure picture.

For instance, if the table of atomic parameters is open in the data pane, clicking on atoms in the structure picture does not automatically select the corresponding atoms in the parameter list. To select the atom(s) in the parameter list basing upon the current atom selection in the structure picture, use the Select in Table command.

This works in a similar way with bonds, contacts, and H-bonds with the tables of bond, contact, and H-bond parameters, rsp., or with table of created molecules or with the tables of atom groups and bond groups.

Selecting atoms, bonds, or contacts from tables

Many of the tables offer commands to select all atoms and/or bonds in the structure picture belonging to the object(s) presently marked as selected in the object table.

Selecting atoms

The table of atomic parameters, as well as the table of atom groups, have special Select Atoms commands to select all atoms in the current structure picture belonging to the atom (or atoms) that are presently selected in the table of atomic parameters or the atom(s) presently selected in the atom group list.

This Select Atoms command is only available from the context menu of the table or atomic parameters and table of atom groups, rsp.

Executing this command resets all previous selection and selects all atoms of the current structure picture that derive from the (one or multiple) atoms that are currently selected in the atomic parameter table or atom group table, rsp.

This command is also available from the context menus of the connection parameter tables (bond, contact, and H-bond parameters) in order to select all occurrencies of the associated atoms each (including symmetry-equivalent positions) in the current structure picture.

There are variants of the Select Atoms command available in the table of atomic parameters: Select Atoms At x,y,z, which regards only atoms of the structure picture at "x,y,z" positions, i.e. atoms that have been created without application of symmetry operations and cell translations, and Select Atoms Not At x,y,z, which regards only atoms of the structure picture that have been created with application of a symmetry operation (unlike the trivial x,y,z) and/or a cell translation.

Selecting bonds

The Select Bonds By Group command is available from the context menu of the table of bond groups. Executing this command resets all previous selection and selects all bonds of the current structure picture that are associated with the (one or multiple) bond groups that are currently selected in the bond group table.

The Select Bonds, Select Contacts, and Select H..A Bonds commands are available from the context menus of the bond parameter table as well as from the tables for contact or H-bond parameters.

Executing these commands resets all previous selection and selects all bonds, or contacts, or H-bonds, rsp., in the current structure picture that derive from the (one or multiple) bonds (contacts, H-bonds, rsp.) that are currently selected in the bond (contact, H-bond, rsp.) parameter table.

Selecting atoms belonging to a least-squares plane or line

The Select Constituent Atoms command selects all atoms in the structure picture that define the L.S. plane or L.S. line, that is currently marked in the table of planes or table of lines, rsp. (This command does not work for pure hkl planes.) A previous selection of other atoms is reset. More information about table and line objects is available here: "Plane and line objects".

Selecting fragments or molecules from atom sites

There are two commands available from the context menu of the atomic parameter list that selects moieties of atoms and bonds belonging together:

The Select Fragments From Sites command selects all symmetry-equivalent atoms of a fragment along with the bonds between the fragments' atoms. A fragment can be any moiety of atoms connected with bonds, regardless if it is part of a molecule or a complete molecule or part of an inorganic or organic polymer. The fragment's atoms are defined by the atoms whose atom sites are currently marked as selected in the atomic parameter table.

The Select Molecules From Sites command selects all molecules in the structure picture where at least one of the currently marked atom sites in the atomic parameter table belong to, meaning it first selects the symmetry-related atoms of the marked atom sites and then completes the selection to the end of the molecules, each. Please note that the command only expands the selection of atoms and bonds. It does not complete a molecule's fragment to a complete fragment, i.e. it does not create the missing atoms and bonds.

Previous article: Selecting objects
Next article: "Atom list": Hierarchical list of atom groups, atom sites, and created atoms of a structure picture

References:
COD:1500005: Hexaammine cobalt(III) hydrogenarseniate tetrahydrate; Ritu Bala, Raj Pal Sharma, Rajni Sharma, Juan M. Salas, Miguel Quiroos, William T.A. Harrison; Journal of Molecular Structure, 828, 174-180 (2007). See sample file "COD-1500005.cif".