Building Schemes
A building scheme is a set or batch of commands to build up a structure picture
Building schemes in brief:
- Several commands available through "Build/Building Scheme" sub-menu.
- "Define Scheme" to define a new scheme or by modification of an existing scheme.
- "Run Proposed Scheme" to run the building scheme that Diamond suggests basing upon structure data.
- Apply Building Scheme from a list in the sub-menu or from the "Run Building Scheme..." dialog.
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Next article: Definition and application of "design schemes" (style sheets)
What is a "Building scheme"
A "building scheme" is a series (or batch) of commands that can be applied to different kinds of structures leading to -- principally -- the same kind of structure picture.
For instance filling a cell range from x=y=z=-1.5 to x=y=z=+1.5 and connecting all atoms (basing on automatically generated and optimized connectivity).
Originally the "building scheme" was already introduced in Diamond version 3, at that time called "Auto-Build".
The "Auto" was renamed to a "scheme" to avoid mismatch with the "Auto Picture Creator", introduced in Diamond version 4, to emphasize that changes in the "Auto Picture
Creator" docking window automatically -- if activated -- reflect
changes in the structure picture.
Location of building scheme commands
Building schemes are managed (added, edited, deleted) in the Building Scheme submenu
of the Build menu. As long
there are no building schemes defined yet, there are only the two commands Define Building Scheme...
and Run Proposed Scheme available in the submenu. The first to define
the first or another building scheme, the latter to apply the building scheme that
Diamond proposes from evaluation of structural parameters. If building schemes have
already been defined, these can directly be applied from the submenu via the Run "<scheme title> commands.
Additionally there is a command Run Building Scheme...
where you can select from a list of building schemes with a short summary of the
scheme that is highlighted in that list each.
(Note: The screenshots have been made with Diamond version 4, the functionality has not changed since then.)
The latest used building scheme is also available from the Picture toolbar, which
is by default positioned at the bottom of the Diamond application window. The sub-menu
for the building schemes can be reached using the dropdown button right beneath
the "last building scheme" icon:
There is also a Building Scheme Manager command available from the Tools menu, so you
can even add, edit or delete schemes while no document is open.
Functions available in a building scheme
The building functions available in a building scheme as well as its title are edited in the Building Scheme Settings dialog.
The checkbox Destroy all atoms, bonds etc. is
activated by default. This is to ensure that all previous contents of the structure picture (except user-defined
text, coordinate system and legend) is deleted before any building operation is
performed. Switch this checkbox off, if you want to keep the current contents and to extend an existing structure picture rather than start from scratch.
The building scheme consists of one basic building function and several additional building functions to modify the basic picture building you can choose.
Choosing the picture's basic building function
The following options are available to create a basic set of atoms (and bonds), you have to choose one of them:
-
Add all atoms (and connections) from parameter list(s)
This option is useful if the atoms in the atomic parameter list describe one or
more complete, isolated structural units (e.g. molecules). On the other
hand, it does not make much sense if the parameter list contains fragments
of a molecule or an inorganic framework. Since in most cases, also bond parameters
are given (typically coming from CIF "_geom_bond_xxx" parameters), the checkbox
Add all bonds is also checked by default, but not the checkboxes Add all H-bonds
and Add all non-bonding contacts, which refer to the H-bond and contact parameters,
rsp., and create all H-bonds and contacts, rsp., together with their associated atoms,
if the corresponding checkbox is checked. See also: "Adding some or all atoms (and bonds) directly". -
Create molecule(s)
This option will create one or more
complete molecules described in the parameter list, even if the molecule(s)
is/are fragmented. The Connectivity
or Atomic Environment settings are
used as a guide to determine bonded atoms, see remarks below.
Note: The molecule generator, which is involved when creating molecules directly from
the atomic parameter (or creating a packing, see below) uses either the bonding spheres from the connectivity
(default setting) or the atomic environments. This criterion can be changed with the command
Build -> Molecules -> Define....
See also: "Generating molecules".
-
Fill cell range
This option treats the atoms in the atomic parameter list as asymmetric unit and applies
all symmetry operations, Bravais translations, and cell translations to create
all symmetry-equivalent atoms in the 3-dimensional range that is given by the
six edit fields x/a-min through z/c-max, given in crystal coordinates.
See also: "Filling cell ranges".
-
Create packing
This option will fill the cell range given by by the fields x/a-min through
z/c-max 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
are determined by the selection in the dropdown box right beneath:
- of molecules with centroid inside: A molecule will be created completely, if its
centroid is inside the cell range.
- of molecules with at least one atom inside: A molecule will be created completely,
if at least one of its constituent atoms is inside the cell range. (This creates
the most molecules typically.)
- of molecules with all atoms inside: A molecule will only be created, if all of
its constituent atoms are inside the cell range.
- with molecules cut at range boundaries: All molecules that are at least partially
inside the cell range will be considered but those parts outside will be cut at
the boundaries.
Like for creating molecules from the atomic parameter list, the connectivity or
atomic environment settings are used as a guide to determine bonded atoms.
See also: "Packing".
-
None
This option should be selected, if the scheme is dedicated to the modification of an existing structure picture
rather than to the creation of a new one. No new atoms will be created a priori.
Choosing additional options
On top of the basic building function, there are several options available for the modification of the structure picture. You can choose multiple of these options:
-
Create cell edges
If this checkbox is activated, the building scheme adds unit cell borders
(or the borders of multiple cells, depending on the settings in x/a-min through z/c-max).
-
Connect atoms
If this checkbox is checked, the building scheme connects all created atoms.
The Atomic Environment settings define the way what and how atoms are connected.
-
Fill coordination spheres around
If this checkbox is activated, the building scheme takes all primarily
created atoms of elements selected in the list to the right, and creates all
atoms within the coordination spheres around these atoms. The sizes of the
coordination spheres depend on the current Atomic Environment settings,
see remarks below. You can use a count > 1 (in the Cycles input field)
to repeat the procedure for the neighbouring atoms in the coordination sphere each.
-
Create polyhedra around
If this checkbox is activated, the building scheme builds coordination
polyhedra around all atoms of elements selected in the list to the right. The
sizes of the coordination spheres depend on the current Atomic Environment settings.
-
Complete fragments
If this checkbox is activated, the building scheme completes molecular
fragments that have been cut during the basic building. Like for creating molecules or a packing, the Connectivity or
Atomic Environment settings are used as bonding criteria.
-
Create broken-off bonds
If this checkbox is activated, ligand atoms created with Fill
coordination spheres around and in the last cycle of the Complete
fragments
function will be hidden and the bonds to these hidden atoms will be drawn
shorter. These "broken-off bonds" pointing into space are often used to
illustrate infinite structures.
See also: "Creating and modifying broken-off bonds". -
Automatic centering
If this checkbox is activated, the center of rotation is automatically placed
into the center of all atoms of the structure picture.
-
Automatic adjustment
If this checkbox is activated, the enlargement factor as well as the position
of the structure picture within the structure window is adjusted to fit the
picture within the window's borders.
Screenshot with "Building Schemes" dialog with a list of available building schemes
and "Building Scheme Settings" dialog opened
Defining a new building scheme or editing or deleting
The command Build -> Building Scheme -> Define Building Scheme... opens
the Building Schemes dialog with the titles of the available building schemes.
If no building scheme has been defined yet, at least "<Proposal>" is available.
Use the Add button to create a new building scheme pre-initialized with the settings
of the building scheme currently highlighted in the list. Use Edit to make changes
to an existing building scheme, or Delete to remove a building scheme (from the
list and from Diamond's Windows Registry section).
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Next article: Definition and application of "design schemes" (style sheets)
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