1. Double-click the Materials Science icon
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory
3. Find your directory, and click Choose
4. Pre-generated input and results files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/builders_crystals.zip
5. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

6. Go to File > Save Project As
7. Change the File name to crystals_tutorial, click Save
   • The project is now named crystals_tutorial.prj

Figure 2-3. Importing .cif files.

While building crystal structures from scratch is do-able (demonstrated in Section 5), it is typically much simpler to begin by importing a structure file. The Materials Science suite supports .cif and .pdb crystal file formats. Some common sources of structure files are:

• The Materials Project Database
• The Cambridge Crystallographic Data Centre (CCDC, CSD)
• Crystallography Open Database (COD)
• Files associated with literature references

In this tutorial, the provided files are .cif and should now be located in your Working Directorythe location where files are saved following Step 7 above

8. Go to File > Import Structures
   • Import panel opens
9. Navigate to the tutorial files and select (Cmd + Click or Ctrl + Click) both alpha-glycine.cif and SiO2_alpha_quartz.cif
10. Click Open
    • The two crystal structures are imported

Figure 2-4. Renamed and reordered imported entries.

Depending on the origin of a structure file, it may have a nondescript name. Such is the case here. Let’s rename and reorder our files

11. Double-click on each name in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to rename the entries as follows:
    • 301K → alpha_glycine
    • a-quartz → alpha_quartz
12. Click and drag the newly named files in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to a new order: alpha_quartz then alpha_glycine corresponding to the order that we will utilize these files in the tutorial
    • The names and order should correspond to the Figure.
13. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue alpha_quartz
    • The alpha_quartz entry will be selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and will appear in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Note: Please refer to the Glossary of Terms for the difference between includedthe entry is represented in the Workspace, the circle in the In column is blue and selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries

Figure 3-1. Applying style settings.

1. With the alpha_quartz entry selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue, in the Style () menu, click ball-and-stick representation and Color Atoms
   • The atoms now appear as spheres rather than points
   • The coloring is updated

Note: The ball-and-stick representation is recommended for viewing solid state structures. As such, this step will always be done first when importing and analyzing crystal structures

Figure 3-2. Menus directly available from the workspace that are useful for crystal structures.

When initially visualizing crystal structures, we will typically use two menus directly available from the workspacethe 3D display area in the center of the main window, where molecular structures are displayed: the Periodic Structure Tool Window () and the Workspace Configuration Panel ()

Note: Whenever a periodic structure is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, next to the button, you will see the associated space group as well as whether you are visualizing the asymmetric unit (ASU). Here the SiO₂ structure in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed is currently the asymmetric unit and the space group is P3₁21 (space group 152)

Figure 3-3. Building a unit cell.

In the next few steps, we will build a unit cellthe repeating pattern in the material having the full symmetry of the crystal structure, which can be infinitely repeated by translation along unit cell vectors from the asymmetric unit. Note that in practice, any of these steps (2-17) can be done concurrently, but we will do them separately to demonstrate the individual role of each selection

2. Click on the button to open the Periodic Structure Tool Window
3. Go to Build Cell
4. Click Apply
   • All of the atoms comprising one unit cellthe repeating pattern in the material having the full symmetry of the crystal structure, which can be infinitely repeated by translation along unit cell vectors are shown
   • Bonding between expected atoms will not necessarily be shown

Figure 3-4. Adding bonds to a unit cell.

5. Click on the button to open the Periodic Structure Tool Window
6. Go to Build Cell
7. Click Recalculate Connectivity
8. Click Apply
   • In addition to all of the atoms comprising one unit cellthe repeating pattern in the material having the full symmetry of the crystal structure, which can be infinitely repeated by translation along unit cell vectors being shown, bonds are included

 

Note: If unexpected bonds are shown (or conversely, expected bonds are not shown), you can manually set the tolerance for bonds from the Workspace Configuration Panel () by adjusting the bond options here:

Figure 3-5. Translating the cell to fit into the unit cell box in the workspace.

9. Click on the button to open the Periodic Structure Tool Window
10. Go to Build Cell
    • Note that Recalculate Connectivity is still selected. Let’s maintain that selection
11. Click Translate to First Unit Cell
12. Click Apply
    • Now, all of the atoms comprising one unit cellthe repeating pattern in the material having the full symmetry of the crystal structure, which can be infinitely repeated by translation along unit cell vectors are shown (again with bonds) and they are translated to the unit cellthe repeating pattern in the material having the full symmetry of the crystal structure, which can be infinitely repeated by translation along unit cell vectors represented by the blue box in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 3-6. Visualizing extents.

 

We will now explore the extents tool. The typical use case for the extents tool is to visualize how the unit cellthe repeating pattern in the material having the full symmetry of the crystal structure, which can be infinitely repeated by translation along unit cell vectors translates in 3D space to generate the infinite crystalline material

13. Click on the button to open the Periodic Structure Tool Window
14. Go to Build Cell
    • Note that Translate to First Unit Cell and Recalculate Connectivity are still selected. Let’s maintain those selections.
15. Click Extents
16. Insert 1 for the +A, +B and +C directions
17. Click Apply
    • An extended view of the crystal is displayed in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • Cell 2 x 2 x 2 is shown in green in the bottom right

Note: We have not changed anything about the crystal structure or its periodic boundary conditions in these steps. Stated another way, these steps are purely visual so far. However, extents should be removed before running a calculation

Note: If you select Create new entry from the Build Cell menu, rather than altering the current entry in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, a new entry will be added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion with the associated build parameters

Note: After doing these steps, you can always deconstruct the cell and return the asymmetric unit by clicking Revert to ASU from the Periodic Structure Tool window

Figure 3-7. Toggling the unit cell box on or off.

A related useful feature is the ability to show or hide the unit cell box

18.   From the Workspace Configuration Panel (), click Unit Cell
    • The unit cell disappears from the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
19. Click Unit Cell again
    • The unit cell reappears
    • Visualizing the unit cell is useful moving forward, so let’s keep this workspacethe 3D display area in the center of the main window, where molecular structures are displayed toggle selected

 

Note: Further display options for the unit cell box are available in the Preferences menu in Workspace > Periodicity

Figure 3-8. Toggling polyhedra on or off.

The polyhedral representation of the model can also be visualized.

20.   From the Workspace Configuration Panel (), click Polyhedrons.
    • Polyhedra appear

For our purposes, we do not need to keep the polyhedra displayed.

21. Click Polyhedrons again
    • The polyhedra disappear

Figure 3-9. Preparing a P1 cell after using the extents tool.

Now suppose we want to transform the original unit cellthe repeating pattern in the material having the full symmetry of the crystal structure, which can be infinitely repeated by translation along unit cell vectors to a new unit cellthe repeating pattern in the material having the full symmetry of the crystal structure, which can be infinitely repeated by translation along unit cell vectors .  There are three typical cases that might warrant doing so:

• To create a larger cell (possibly of a different shape).
• To create a cell representing the crystal system under stress or strain.
• To create or manipulate a cell with a vacuum gap (for example for slabs or molecule in the box models)

Each case requires careful thought before redefining the lattice. The first case, creating a larger cell, is the most common transformation (for example, to prepare an appropriate sized unit cell to study adsorption of a small molecule) and is straightforward. For integer extent expansions, this can be done directly in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

22. Click on the button to open the Periodic Structure Tool Window
23. Select Make P1 Cell
    • The unit cell is now what was the 2 x 2 x 2 supercell displayed earlier
    • The bottom right indicates that this is now the ASU in the P1 space group
    • A new entry has been added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled alpha_quartz P1 and is includedthe entry is represented in the Workspace, the circle in the In column is blue by default

Note: Because we are now fundamentally altering the periodic boundary conditions associated with our original crystal, a new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion (alpha_quartz P1) so that we also retain our original structure (alpha_quartz). In this case, the structures are fundamentally the same in the context of the infinite crystal, but they are defined by different sized unit cells

Figure 3-10. The Redefine Lattice panel.

Optional: To conclude this section, we will learn how to use the Redefine Lattice panel to transform the cell to represent a system under stress or strain. Feel free to skip to Section 4 if this topic is not relevant

24. Go to Tasks > Materials > Tools > Redefine Lattice
    • The Redefine Lattice panel opens
    • So long as the alpha_quartz P1 entry is includedthe entry is represented in the Workspace, the circle in the In column is blue, the cell parameters are loaded into the panel

Suppose we wanted to prepare a crystal that is uniaxially strained along the a-axis

25. Keep the Set new cell parameters radio button checked, adjust a to 10.02, and press enter (representing a hypothetical ~2% strain from the original a = 9.828 Å)
    • The Transformation Matrix automatically updates
26. For Transformation mode, select Strain (fractional coordinates are fixed)
27. Click Run
28.  
    • A new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. It is both selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue, and is named alpha_quartz P1

Figure 3-11. The P1 cell after the cell parameters have been redefined.

29. Close the Redefine Lattice panel
30. Rename this entry alpha_quartz P1_strained

Note: We have now fundamentally altered the periodic boundary conditions and cartesian coordinates associated with our original crystal. Doing so requires caution. An optimization is always suggested before performing any property calculations on a crystal structure. This is especially true after altering periodic boundary conditions

Figure 4-1. Select and include alpha glycine.

1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue alpha_glycine from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
   • The alpha glycine crystal structure appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-2. Updating style.

2. In the Style menu, click ball-and-stick representation and Color Atoms
   • The atoms now appear as spheres rather than points
   • The coloring is updated
3. From the Color Atoms dropdown, select Element
   • The atoms are colored by element

Figure 4-3. Building a cell.

As was the case for inorganic structures, the Periodic Structure Tool Window () allows visualization of the periodic system:

4. Click on the button to open the Periodic Structure Tool Window
5. Select Build Cell
6. Select all four of the options
   • Within Translate to First Unit Cell, select Intact Molecules
   • For extents, add 1 for +A and +B to create a 2 x 2 x 1 supercell.
7. Click Apply
   • A new supercell appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

Note: Choosing Intact Molecules in the Translate to First Unit Cell section translates the molecules so that all of their centroids are in the unit cell, allowing visualization of complete molecules rather than fragments

Feel free to explore visualizing and manipulating the organic system analogously to our steps in Section 3.

Figure 5-1. Reset the builder panel.

1. Go to Tasks > Materials > Structure Builders > Crystal Structure
   • The New Crystal Structure panel opens
2. If the panel is populated with data from one of the previous steps, simply click Reset in the bottom left corner of the panel
   • All inputs return to their default settings

Figure 5-2. Defining NaCl in the builder.

The space groupthe point group operations (reflections and rotations) and translations that define the unit cell, periodic boundary conditions and fractional coordinatesa coordinate system for the position of atoms in the basis of the unit cell vectors associated with NaCl are provided in the following steps. Populate the panel with the following information:

3. Space Group Number: 225
   • F 4/m -3 2/m appears
4. Lattice Parameters:
   • a = b = c = 5.64 Å
   • ɑ = β = ɣ = 90º
   • Some parameters are fixed, as dictated by the space group
5. Within Asymmetric unit, click Add Atom twice
   • Two C atoms are added by default
6. Click on the first C to update the first atom to Na and repeat to update the second atom to Cl
7. The Na ion should have the fractional coordinates (0 0 0) and the Cl ion should have the fractional coordinatesa coordinate system for the position of atoms in the basis of the unit cell vectors (0.5 0 0). Update the f1, f2 and f3 entries accordingly as needed
   • Fractional coordinatesa coordinate system for the position of atoms in the basis of the unit cell vectors is defined in the Glossary of Terms
8. Maintain the remaining defaults. The panel should match that which is shown in the Figure
9. Click Create Crystal Structure
10. Title it NaCl
    • A new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. Although only two atoms were specified (the asymmetric unit), eight atoms are generated (the full unit cell) due to the symmetry operators applied to the asymmetric unit
11. Click OK
12. Close the panel

Figure 5-3. Updating the style.

13. In the Style () menu, click ball-and-stick representation
    • The atoms now appear as spheres rather than points
14. If anything is not to your visual liking with respect to bonds and connectivity, refer to Section 3 and feel free to experiment with viewing and manipulating the NaCl structure

Figure 5-4. A snippet of some of the data available in the Project Table.

We may be interested in the volume or density of this cell. We also may also wish to see the lattice parametersthe lengths of the unit cell vectors (a, b, c) and angles between them (ɑ, β, ɣ) which define the unit cell for any crystals in the project all in one place

15. Open the Project Table ()

Notice that for all of the structures, the unit cell density, unit cell volume, space group and lattice parameters are shown

Note: To add or remove columns from the Project Table, the Property Tree () is a useful tool

16. Close the Project Table ()

Figure 6-1. Building a larger cell.

1. With the NaCl entry selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue, click on the button to open the Periodic Structure Tool Window
2. Click Build Cell 
3. Select Recalculate Connectivity
4. Select Extents and input 1 in the +A, +B +C, -A, -B, and -C directions
5. Check Create new entry and then click Apply.
   • A new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion named NaCl by default
   • The entry is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue
   • The structure in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed now includes 216 atoms.

Figure 6-2. Renaming the entry.

6. Rename the entry by double-clicking on the new NaCl in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and typing NaCl_vac

Figure 6-3. Duplicate the entry.

7. Right click on NaCl_vac and click Duplicate > In Place
   • Another entry named NaCl_vac is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
8. Rename this entry (as in Step 6): NaCl_dop
   • Your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion should now includethe entry is represented in the Workspace, the circle in the In column is blue three entries related to the NaCl crystal:
     • The original unit cell with 8 atoms (NaCl)
     • The 3 x 3 x 3 cell with 216 atoms (NaCl_vac)
     • The same cell with 216 atoms (NaCl_dop)

Figure 6-4. Setting the selection scope to atoms.

First let’s introduce vacancies manually.

9. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue NaCl_vac

Make sure your current selection scope is Atoms (it may still be Molecules depending on which previous steps you have completed):

10. Set the selection scope to Atoms using the menu in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed or by typing a on your keyboard
    • The cursor updates to notify you that atom selection is active

Figure 6-5. Selecting and deleting a Na and Cl ion.

11. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries one Na ion and one Cl ion in the lattice (using Shift + Click)
    • A selection box appears around the selected ions
12. From the Build menu (in the Toolbar), click delete selected atoms
    • The selected ions are deleted from the structure. You have now created a Schottky defect

Note: In practice, from here you must create a new P1 cell before proceeding to calculate properties of the crystal structure with these vacancies.

Note: Vacancies can be introduced more systematically in the Crystal Builder panel (without deleting the original coordinates) by changing the occupancy of an atom to 0%

Figure 6-6. New P1 cell with a centered unit cell.

Let’s look at one final useful case, to introduce a substitutional dopant

13. Now, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue NaCl_dop

If you wanted to replace one Na ion with a K ion, you could use a similar process to the previous steps with the Build menu. In this case, let’s make this alteration slightly differently to demonstrate using the Crystal Builder panel:

14. Click on the button to open the Periodic Structure Tool Window
15. Select Make P1 Cell
    • A new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion named NaCl_dop P1.
16. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue NaCl_dop P1.
17. If the unit cell box is not properly centered, center the cell in the Workspace Configuration Panel ()

Figure 6-7. Substituting one Na ion for a K ion.

18. Go to Tasks > Materials > Structure Builders > Crystal Structure
    • The Crystal Structure panel opens
19. Click Load from Workspace
    • The asymmetric unit is populated with the atoms comprising the P1 cell from the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
20. Change one of the Na atoms to K by clicking on the Na element button in the table and using the Choose Element panel
21. Click OK
22. Click Create Crystal Structure
23. Name the structure NaCl_dop_K
24. Click OK
25. Close the Crystal Structure panel

 

Figure 6-8. Selecting the K ion.

26. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue Na_Cl_dop_K
27. In the Style menu, click ball-and-stick representation
    • The atoms now appear as spheres rather than points

The K default color happens to be the same as Na. Let’s use a convenient selection method to locate the K ion and change its color to purple

28. From the main menu, go to Select > Define
    • The atom selection panel opens
29. Click Element, K and then Add
    • K appears in the ASL box
30. Click OK
    • The potassium ion will now be selected in the crystal structure

Note: Selecting atoms via this method is quite useful when seeking particular selections in large structures

Figure 6-9. Coloring the K ion.

31. In the Style menu, use the paint tool to color the selected atom purple
    • The K ion turns purple

Figure 6-10. The Assign Space Group panel.

After making a new P1 cell and manipulating the structure (in this case substituting one Na ion for a K ion), it may be practical to assign a space group to the new structure - the assignment of the space group is mainly useful for reducing the cell to a primitive cell.

32. With NaCl_dop_K selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue, go to Tasks > Materials > Tools > Assign Space Group
    • The Assign Space Group panel opens
33. Click Run
    • New entries are added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion which can be stylized again as needed
34. Close the Assign Space Group panel
35. Open the Project Table ()
    • You should notice that the new structure has Space Group ID 221

Figure 7-1. Import, rename, select and include the zinc complex.

1. Go to File > Import Structures
   • Import panel opens
2. Select Section_07 > 1510909.cif
3. Click Open
   • The crystal structure is imported
4. Rename the entry:
   • Cm48usa → Zn_Disorder
5. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue Zn_Disorder from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
   • The Zn_Disorder crystal structure appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 7-2. Select, include and stylize Zn_Disorder.

6. In the Style menu, click ball-and-stick representation and Color Atoms
   • The atoms now appear as spheres rather than points
   • The coloring is updated

Notice that the oxygen atoms on the perchlorate ligand and anion were modeled with disorder. Also notice that the hydrogen atoms are not necessarily bonded by default

 

Figure 7-3. Building the unit cell for the Zn system.

7. Click on the button to open the Periodic Structure Tool Window
8. Select Build Cell > Recalculate Connectivity and Recalculate Bond Orders
9. Click Apply
   • An error appears “Atoms with disorder group found”
   • Click OK
10. Click Open Crystal Builder

Figure 7-4. Resolving the disorder.

If you scroll through the atoms in the asymmetric unit, you will notice that some of the oxygen atoms have partial occupancies (< 1.0)

11. Click Create Crystal Structure
    • A drop-down appears for handling the disorder
12. Select which group of atoms you would like to include with full occupancy, and in doing so, which group will be erased. A radio button appears alongside either group with which to make the selection. In this case, let’s choose the top radio button because the occupancies are a bit higher
13. Click OK
14. Again click Create Crystal Structure
    • A warning appears that the atoms in the excluded group will now have zero occupancy
15. Click OK
16. Rename the entry Zn_Disorder_occ
17. Click OK
18. Close the panel
    • The crystal structure includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed (Zn_Disorder_occ) now only contains one set of oxygen atoms at the disordered perchlorate sites and can now be stylized, visualized and used for subsequent calculations