Quick Start Guide for CrystalExplorer 3.0
|Note: The screenshots shown in this guide are taken from the Mac OS X version of CrystalExplorer. You may see small differences in how the program appears in the Windows and Linux versions. However the functionality of CrystalExplorer remains the same regardless of the operating system.|
What is CrystalExplorer?
CrystalExplorer is a standard tool for investigating intermolecular interactions and packing in crystalline materials using Hirshfeld surface analysis.
CrystalExplorer also includes powerful tools to generate surfaces based on ab initio quantum mechanical property densities.
By mapping these properties and other distance- and curvature-related metrics on Hirshfeld surfaces, CrystalExplorer provides unique insights into the in-crystal environment.
A recent feature in this version is the ability to display and quantify voids in crystal structures.
CrystalExplorer reads crystal structures from Crystallographic Information Files (CIF).
To open a CIF, either
Each time a CIF is opened, CrystalExplorer adds all the crystal structures contained within it to the current project.
A list of all the crystal structures is shown in the selection box in the top-right of the main window.
Clicking in the selection box on a chosen crystal will cause it to be displayed in the graphics window.
|Tip: The easiest way is zoom in/out is to use your scroll-wheel on your mouse.|
CrystalExplorer allows you to rotate, zoom in/out and translate so that you can achieve a particular orientation of the structure.
By default CrystalExplorer starts in the rotation mode. To rotate the structure, left-click in the graphics windows in the background, and drag the mouse around.
Since left-clicking is also used to selected atoms/molecules is important to only left-click on the background if you want to change the view.
When in the rotation mode it is also possible to rotate about the z-axis (out the screen) by holding down the shift key and left-click-dragging the mouse.
The View Toolbar
The view toolbar, shown below, appears the the bottom of the graphics window.
Using the view toolbar, you can precisely rotate or scale the structure.
|Tip: When one of the rotation angle boxes in the toolbar is highlighted, you can rotate about his axis by hovering the mouse over the angle box and rotating the mouse wheel.|
Or, you can choose a view down one of the crystallographic axes a, b or c.
The recenter button resets the center of rotation to be at the center of the atoms displayed.
Recentering is useful after a large, asymmetrical cluster has been created.
Atoms and molecules need to be selected before surfaces or clusters can be made.
An atom is selected when it is highlighted by a golden mesh.
Select atoms and molecules by left-clicking on them:
- To select a single atom, left-click on it.
- To select a whole molecule or fragment, double left-click on an atom or bond.
- To select everything, right-click to bring up the context menu and choose the menu item Select All Atoms.
To help with choosing atoms you can show the atom labels.
By repeating the left-click operation an item can be deselected.
Left-clicking in the background of the graphics display is the fastest way to deselect everything.
CrystalExplorer provides a number of methods for building up clusters of atoms or molecules.
Many options in CrystalExplorer can produce 'incomplete' molecular fragments.
Indeed, a cif file may contains only an incomplete asymmetric molecular fragment.
Click this button on the main toolbar to generate all the atoms in the unit cell.
You can also show the bounding box of the unit cell by choosing Options→Show Unit Cell Axes from the main menu or Show Unit Cell Axes from the context menu.
This button generates multiple copies of the unit cell including any surfaces which you have made within.
A dialog box allows the user to choose the number of copies and direction in which to make the unit cell copies.
This is useful when combined with crystal void surfaces to show empty pores and channels in the structure.
These gjhosts representing atoms close to the real atoms shown in the graphics window.
By left-clicking on the ghosts, they become real atoms, and a new set of close-contact atoms is displayed.
By repeated clicking on the ghost atoms, the connectivity of the crystal structure can be explored.
In this way, the cluster of atoms representing the crystal structure can be expanded.
The ghost atoms are turned off by clicking the close contact button again.
This feature allows the user to generate a cluster of atoms within a specified distance of any atom currently selected.
When the button is clicked, a popup window appears; simply enter the desired distance.
|Tip: Selecting a zero distance when making a radial cluster eliminates all atoms except those selected|
CrystalExplorer can generate the following surfaces:
- Crystal Voids
- Electron Density
- Deformation Density
- Electrostatic Potentials
- Molecular Orbitals
One of the most powerful features of CrystalExplorer is the ability to map properties onto surfaces with color. Some of these properties e.g. the electron density property must be chosen when generating the surface but there are a number of built-in properties that are always available to these surfaces. At present only Hirshfeld, promolecule and electron density surfaces can have properties mapped onto them.
|Tip: When generating crystal void surfaces select any atom and generate the surface. The selection doesn't matter because CrystalExplorer generates a new cluster specially for the calculation of void surfaces.|
General procedure for generating surfaces is:
- Using the mouse, select the atoms you want included in the surface. In general you'll want to select a complete though CrystalExplorer will often allow surfaces to be generated for any selection including single atoms.
- Click the toolbar button to bring up the surface generation dialog.
- In the surface generation dialog you must choose the surface type, any surface properties and the resolution (quality). Surfaces can be further customised with surface options e.g. the surface's isovalue. Click the ok button to generate the surface.
Some of the surfaces and surface properties are quantum mechanical in nature and require a wavefunction. CrystalExplorer automatically brings up the wavefunction calculation dialog when a wavefunction calculation is required.
Wavefunction calculations can be performed with the built-in Tonto program or with Gaussian program. In order you CrystalExplorer to be able to use Gaussian follow these the steps on the "Setting up Gaussian" page. Note: Gaussian isn't distributed with CrystalExplorer and must be purchased separately.
All generated surfaces appear in that crystal's surface list. A green tick next to a surface name tells CrystalExplorer to show that surface in the graphics window. By clicking on the green tick, it will be changed to a red cross and the surface will be hidden from view. This is useful if you have many surfaces and only want to keep the display from getting cluttered.
The Surface Controller (located at the bottom right hand side of the CrystalExplorer Window) gives you details about the surfaces and allows you to change features of the surface ― for example, which property is currently mapped on its surface. The Surface Controller has three tabs,
- Options Tab: allows you to set all aspects of the surface, including the property mapped on the surface, the color range for the property, and whether the surface is displayed semi-transparent.
- Info Tab: displays information such as the area and volume of a surface.
- Property Info Tab: provides certain statistical information about the property on the surface. By default the min, max and mean of the property on the surface is shown. Detailed statistics can be provided by clicking on the "All Statistics" button.
|Note: All fingerprint plots should come from Hirshfeld surfaces generated at high resolution. Lower resolutions produce meaningless fingerprint plots.|
To display a fingerprint plot, first select a Hirshfeld surface (in the surface list) and then click on the Fingerprint Button . This button is located in the Surface Controller in the bottom right of the CrystalExplorer window.
The fingerprint window includes options for,
- Translating or expanding the fingerprint plot to cater for structures with longer distance contacts.
- Saving the fingerprint plot.
- Creating decomposed fingerprint plots.
Decomposed Fingerprint Plots
Decomposed fingerprint plots are produced by applying a filter to highlight only close contacts between atoms of a particular chemical elements. Only contributions of those interactions are shown in the fingerprint plot with the rest greyed out.
By clicking on the fingerprint plot, highlight "cones" can also be displayed on the Hirshfeld surface showing which points on the surface correspond to a certain di/de pairs
For more information, see Fingerprint Plots.
CrystalExplorer includes tools for conventional structure analysis.
You can measure distance and angle between objects by clicking on the appropriate toolbar buttons before selecting your objects to measure.
- Select two atoms (using left-click); the atoms are highlighted in green and the distance is shown.
- Select an atom then (left) click a point on a surface; the distance between the atom and the selected surface point is shown.
- Tip: Double (left) click on an atom or a surface; then single or double (left) click on another atom or surface; the minimum distance between the two objects is shown. Nice.
- Select three atoms in sequence. An arc will be drawn between the first and third atoms, with the second atom at the centre. The angle will be displayed on the screen.
- For the dihedral angles, in-plane and out-of-plane bends you need to select four atoms. These angles include a translucent green plane to help the user visualise the angle. This translucent green plane is best viewed on a non-white, non-black background.
Right-clicking in the graphics windows brings up the context menu and allows fast access to many common operations.
The options presented depend on whether you right-clicked on the background, an atom or a surface i.e. they depend on the context in which you right-clicked.
- Charge and multiplicity of selection
- M.A. Spackman, J.J. McKinnon, CrystEngComm, 2002, 4 ,378-392:
Fingerprinting Intermolecular Interactions in Molecular Crystals
- Generally want to save the fingerprint as an .eps for publication purposes
- J.J. McKinnon, D. Jayatilaka, M.A. Spackman, Chem Commun., 2007 ,3814 - 3816:
Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces