Detailed View
The detailed view provides a comprehensive summary of the most important features of an entry. Select the data set(s) you wish to investigate: Use the checkboxes in front of the entries (Fig. 1, (1.)) or click on “Select All”/”Deselect All” to select/deselect all entries (Fig. 1, (2.)). The button “Show Detailed View” will be activated (Fig. 1, (3.)).
Clicking on the button “Show Detailed View” will show the selected data sets in detailed view mode (Fig. 2). The window consists of 3 main parts:
1. The navigation shows what entry is currently displayed, in this case “Entry 1 of 1” (Fig. 2, (1.)). The arrow buttons allow the user to jump to the first selected entry, to turn to the previous entry, to the next entry and to the last entry, respectively. The button “Back to List View” shows the result list without erasing the current query. The button “Back to Query” erases the current query and jumps back to the search mask.
2. The summary gives a brief description of the main features of the currently displayed entry, such as ICSD Collection Code, unit cell data, reference etc. (Fig. 2, (2.)). The fields are also shown in the “Details” section, and will be described there. It is possible to export the current entry as a CIF (Crystallographic Information File) from here.
If 2 or more entries are selected, a Synoptic View can be accessed, too.
3. The Detailed View gives a complete and comprehensive listing of all important entry data (Fig. 2, (3.)). It is possible to expand individual fields by clicking on the desired caption, to expand all fields (“Expand all”) or close all fields (“Collapse all”). The individual detail fields will be described hereafter.
In addition the Print link next to the logout option in the title bar will generate a properly formatted pdf-file containing the complete information found for this entry in the Detailed View.
Figure 2: Main parts of the detailed view. (1.) Navigation bar, (2.) Summary, (3.) Details for several aspects of the selected crystal structure
Description of fields in section “Details”
The Visualization field consists of a crystal structure display (Fig. 3, (1.)) and a powder pattern display (Fig. 3, (2.)) part.
The crystal structure display makes use of the Jmol [1] applet, showing the most important data within the display box: Sum formula, space group and lattice constants as published by the author(s), and a 3D picture of the unit cell.
Right-clicking into the structure display box opens a pop-up menu, from where the user is able to change display properties as well as performing geometric analyses of the displayed structure.
Additionally, the crystal structure can be displayed in a separate window (“Display in Window”).
Clicking on “Configure Structure Display” opens a new field with possibilities to manipulate display options for the current crystal structure:
Display Content: A dropdown box allows for atom display customization. Hydrogen bonds, polyhedral and/or cavities can be shown by selecting the appropriate box. The Select checkbox lets you highlight the equivalent atoms in the display by clicking on one atom.
Display Properties: Allows changing certain aspects of displaying the crystal structure, such as background (on/off), perspective drawing (on/off), stereo (red/green) display. “Spin” will let the currently displayed structure rotate around the vertical axis. “Display Labels” will put the atom labels beside the appropriate atom.
Unit Cells: Enter the number of unit cells for each lattice direction you want to have displayed. Note: Although it is possible to enter decimal fractions, the fractions will be cut off. The values for abc are limited to 1.0 - 4.0.
It is necessary to click on “Redraw Display” after making changes in the number of unit cells displayed along each lattice direction or in the radii limits for drawing bonds.
Three additional buttons allow for customization. You can save your preferred settings for structure display with Jmol by pressing the "Save As Default"-button. Clicking the "Restore Default"-button changes the display properties to your previously saved defaults or to the system defaults if you have no saved defaults. The "Reset to System"-button will always restore the properties to the original defaults.
Bonds: The generation and display of bonds can be limited either by defining minimum and maximum distances or by providing minimum and maximum percentages of the sum of the ionic radii of the involved atoms/ions.
Figure 3: Crystal structure display (1.) and powder pattern display (2.)
The right part of the Visualization window shows a simulated powder pattern of the currently displayed crystal structure. The caption shows the ICSD collection code.
You have the option to display the powder pattern in a separate window, export it as a two-column x-y data file or to export it as a PDF file. In addition you can create a table with hkl, 2 theta, d, multiplicity and intensity for each reflection in a txt-file.
Clicking on “Configure Powder Pattern Calculation and Display” opens a new field, enabling the user to influence calculation and visualization parameters for the powder pattern.
The drop down box “Radiation Type” contains radiation sources (neutrons or X-rays) as well as experimental setups (Debye-Scherrer, Guinier-de Wolff, Guinier-Hagg).
It is possible to enter either a custom wavelength (Angstrom units) or select one predefined from the drop down box (Cu, Cr, Fe, Mo, Ag).
The reflex profile parameters U, V and W can be changed. Toggling between line diagrams (checkbox “Intensities only”) and standard powder patterns (Gauß envelope) is possible, too.
You can choose between 2 plot types: 2theta and 1/d. 2theta plots in the range 0.1-60° in 0.1° steps are shown per default. xmin, xmax, and xstep describe the starting, the ending and the step value according to the chosen plot type, respectively.
Additionally, it is possible to display the corresponding indices for each reflection as well as colour the powder pattern in red.
It is necessary to click on “Update View” after making any changes.
Chemistry
The “Sum Form” field shows the sum formula with all stoichiometric coefficients, where the elements are sorted in the order C, H (D), (rest of the elements in alphabetic order). In the field “Struct. Form.” (Structured Formula – not Structural Formula!) certain building blocks of a chemical compound are grouped, e.g. Ca (C O3) (H2 O)6, where the sum formula would show C1 H12 Ca1 O9.
The chemical name, the mineral name and the mineral group are listed accordingly. The number of formula units (Z) shows how many times the unit cell contains the atoms in the field “Sum Form”.
The ANX formula is generated according to the following rules (see Tab. 1 for examples):
- H+ is not taken into account, even if coordinates are available.
- The coordinates for all sites of all other atoms must be determined.
- Different atom types on the same position are being treated as one single atom type. The relevant atom type is the one with the highest site occupation factor (SOF). If the SOFs are equal, the first atom type is the relevant atom type.
Exception to this rule: if anions and cations occupy the same site they will not be treated as one atom type. - All sites occupied by the same atom type are combined unless the oxidation state is different. Fe2+(Fe3+)2O4 → AB2X4
(Fe2.6667+)3O4 → A3X4 - For each atom type the multiplicities are multiplied by the SOFs and the products are added. The sums are rounded and divided by the greatest common divisor.
- If the rounded sum is equal to zero all sums are being multiplied by a common factor so that the smallest sum is equal to 1.0, so no element will be omitted.
- Cations are assigned the symbols A–M, neutral atoms N–R and anions are assigned X, Y, Z, S–W.
- The symbols are being sorted alphabetically and the characters are assigned according to ascending indices: AB2X4, not A2BX4.
- All ANX formulae with more than 4 cation symbols, 3 neutral symbols or 3 anion symbols are deleted. This measure limits the number of different ANX formulae.
Table 1: Examples for ANX formulae
Chemical formula | ANX formula |
|---|---|
Mg3Al2(SiO4)3 | A2B3C3X12 |
Ca3(Al1.3325Fe0.6675)Si3O12 | A2B3C3X12 |
(Mg2.7Fe0.3)(Al1.7Cr0.3)Si3O12 | A2B3C3X12 |
Figure 5: Published (1.) and Standardized (2.) Crystal Structure data
The field “Published Crystal Structure Data” (Fig. 5, (1.)) shows the crystallographic information as given by the author(s). Among the cell parameters, space group, crystal system, crystal class, Laue class and Pearson symbol you will find the cell volume, number of formula units (Z) and structure type information.
The list of atomic coordinates is also contained.
The “Standardized Crystal Structure Data” (Fig. 5, (2.)) is derived from the published data and gives information on the same fields as above. The standardization is done following the rules given by L. M. Gelato and E. Parthé in J. Appl. Cryst. (1987) 20, 139-143.
Distances and Angles
The distances and angles dialogue enables the ICSD user to perform statistical analyses of interatomic distances and angles. You can either choose from the element type lists or from the atom position lists. The maximum search range (Rmax) is 5 Angstrom for distances and 200% for the sum of ionic radii.
Figure 6: Distances and Angles screen: selection by elements
Figure 7: Distances and Angles screen: selection by atom positions
When at least one element/atom position each in Atom A and Atom B is selected, the user may click the “Histograms” or the “Calculate” button.
“Calculate” will generate a list of bond length if only Atom A and Atom B contain selected element/atom positions (Fig. 6, Fig. 7). Bond angles are calculated if in addition at least one element/atom position is selected in the Atom C field.
Switching to the “Histograms” view (Fig. 8) shows 2 windows. The upper one shows the number of occurrences of interatomic distances of the selected pair(s) of atoms in the whole database. The interatomic distance(s) found in the current entry are marked blue; they are explicitly shown in the lower window. While the x-axis shows distances in Angstrom units, the y-axis shows the number of occurrences.
Figure 8: Histograms of interatomic distances
The bond length dialogue consists of a text-only list of interatomic distances within the defined range, including oxidation states, Wyckoff symbols and the symmetry operation necessary to create Atom B (Fig. 9). Please note, that the translational part is encoded. 555 is the current unit cell. If 1.0 is added to the y-coordinate, 555 becomes 565. A number 456 means that 1.0 is substracted from the x-coordinate and 1.0 is added to the z-coordinate.
Figure 9: A text-only list of interatomic distances
The dialogue for bonds and angles shows a text-only list of interatomic distances as above as well as a list of bond angles. The angles list consists of the atom, oxidation state and Wyckoff symbol as well as for all atoms the symmetry operation necessary to generate Atoms B and C (ig. 10).
Figure 10: Bonds and Angles results list
Bibliography
Fig. 11 shows the “Bibliography” information of the current entry: Title and reference(s). The “Get full text” link provides a connection to the publication for the current entry.
If your institution has a SFX link resolver installed you can provide us with the necessary information (URL of the server and URL of a small logo). In this case your logo and an optional descriptive text is displayed and requests for original articles are redirected to your SFX link resolver.
This implementation of OpenURL is compatible with link resolvers like SFX or with document delivery services like FIZ Autodoc.
Experimental Information
The section “Experimental Information” is divided into 3 subsections (Fig. 12):
1. External conditions
The ambient pressure and temperature are given as published by the authors. Note: If no pressure or temperature were published, default values of 0.101325 MPa and 293 K are assumed and added. The corresponding fields for temperature and pressure will then contain "room temperature" and "atmospheric", respectively. The radiation type can be: X-ray, electrons, neutrons or synchrotron. The sample may either be a polycrystalline powder or a single crystal. The R values of a subsequent structure refinement are given if available.
2. Additional Information
If published, the entry may additionally contain information about twinning of crystals, theoretically calculated structures, available NMR data, performed Rietveld refinement, available magnetic structure, correction of earlier work(s), determination of absolute configuration and/or available anharmonic temperature factors.
3. Properties of Structure
This subsection shows whether or not the current structure is polytypic, disordered, a defect structure, a misfit layer structure, a mineral and/or a structure prototype.
Figure 12: Experimental Information
Warnings and Comments
Figure 13: Warnings and Comments
The “Warnings and Comments” field informs the user about (probable) inconsistencies (wrong coordinates, atoms too close etc.) of the current structure. Additional comments (stability of the compound etc.) are mentioned, too (Fig. 13).
Compare Published and Standardized Structure
Fig. 14 shows the published and the standardized structure side-by-side for easy comparison of both. The same configuration possibilities as for the visualization (see above) apply.
Figure 14: Comparison of published and standardized structures
[1] Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/