Endeavour
Structure Solution from Powder Diffraction
Endeavour is a powerful software for crystal structure solution, both from powder as well as single crystal diffraction data. Based on more than ten years of experience, the software is capable of solving many small to medium sized structures more or less on its own. The innovative concept combined with the elaborate user interface makes the solution of crystal structures an almost routine process, especially for inorganic but also for many organic compounds.
Even unexperienced users can prepare and perform the structure solution calculation in a few steps: Simply follow the integrated "wizard" to enter the required data (unit cell parameters, chemical composition, diffraction data), and let Endeavour do the rest. The structure solution is performed using a special variant of the "direct-space" approach, namely a combined global optimization of the difference between calculated and observed diffraction data and of the potential energy of the system. Due to the additional usage of the potential energy, the method is much less sensitive to low-quality diffraction data than e.g. direct methods.
The latest version 1.8 with a re-designed user interface brings several improvements and bug fixes.
Scientific background
Details about the scientific background of Endeavour have been published in Journal of Applied Crystallography: H. Putz, J.C. Schoen, M. Jansen, and Combined Method for "Ab Initio" Structure Solution from Powder Diffraction Data, J. Appl. Cryst. (1999), 32, 864-870.
Purpose
Crystal structure solution from powder or single crystal diffraction data using a combined global optimization of the difference between calculated and measured diffraction pattern and of the potential energy of the system ("Pareto optimization").
Functions
Structure Solution:
- Structure solution from conventional X-ray laboratory diffractometer as well as synchrotron, neutron or electron diffraction data
- Input required:
- unit cell parameters
- diffraction data: either powder diffraction data (integrated intensities at Bragg angles (not profile/step-scan data), imported from Philips, Bruker-AXS, Stoe), or single crystal diffraction data (I(hkl), |F(hkl)| or F2(hkl)), e.g. imported from SHELX-file
- contents of the unit cell (composition or molecular structure plus number of the formula units)
- "Wizard" for the easy preparation of the input data
- Automatic adjustment of all structure solution calculation parameters
- Calculation of profile patterns from experimental and calculated peak lists, instead of just comparing the intensities of correlated peaks. By doing so, the R-factor calculation is much less sensitive to 2theta errors and wrong peak assignments. In earlier versions of Endeavour, this problem frequently lead to wrong R-factor values and could prevent a whole crystal structure from being solved.
- Automatic space group determination from resulting structure
- Optional or automatic check/correction of 2theta errors.
- Automatic checking of peak correlations (optional, active by default).
- Several "advanced settings", e.g. flexible molecules, jump widths, peak triangles, Simulated Annealing parameters etc. - available from the structure solution wizard.
- Crystal structures containing molecules/rigid bodies can now be solved directly in a space group other than P1, even if their atoms must be placed on special positions.
- Viewing of the intermediate steps of the structure solution process: progress (% finished), R-Value and overall cost function, list of correlated calculated and observed peaks, structure picture, and diffraction diagram in user-defined arrangement side-by-side.
- Auto Build function to visualize the crystal structure of each intermediate step, e.g. the unit cell, with or without bonds, with or without polyhedral, molecules, etc.
- Report View displaying the results of Pareto optimization as formatted text that can be copied to clipboard, saved, or printed.
- Easy editing, calculation, and fitting of potential parameters (simple repulsion, Lennard-Jones).
- Minimum interatomic distances for all element pair combinations (derived from Pearson's Crystal Data) are now implemented (no need for manual adjustment of parameters for the simple repulsion potential anymore)
- Support for molecular as well as for atomic crystal structures. Molecules can be fixed at certain positions and may rotate along a reference atom.
- Symmetry Finder with automatic or interactive transformation to higher space group.
- "Structure Solution" by either energy minimization or diffraction data alone is possible. Manual selection of rotatable bonds within the molecule(s) for variation during structure solution calculation.
- Import of 3-dimensional molecular structures from various file formats including Diamond (*.dsf), Cambridge CSD-FDAT (*.dat, *.fdat, *.csd), MDL Molfile/SDFile (e.g. from ACD ChemSketch) (*.mol, *.mdl, *.sd), Cerius2 CSSR (*.cssr, *.dat), Sybyl MOL/MOL2 (*.mol, *.mol2) and CIF (*.cif) files.
- Molecules can also be sketched and transformed into 3D using ACD ChemSketch Freeware which can be installed from the Endeavour 1.x CD-ROM.
Structure Visualization:
- Settings for the structure visualization "Autobuild" function (e.g. molecules, polyhedral) are now adjusted automatically, taking into account the "chemistry" of the compound under investigation
- Manual input or change of structural parameters and bibliographic data.
- Imports structure data from crystal structure databases (Inorganic Crystal Structure Database, Cambridge Structural Database, Protein Data Bank), from Pauling File (Inorganic Material Database), from Crystallographic Information File (CIF), from SHELX format, as well as from several molecular structure formats.
- Creating contents of unit cell, super-cell, or any arbitrary range of the crystal lattice.
- Discussion of connectivity assisted by histograms showing the distribution of distances between selected atom types, together with automatic calculation of distance ranges.
- Completion of coordination spheres around selected atoms.
- Generation of molecules or completion of molecular fragments that have been clipped at the cell edges (packing diagrams).
- Ball-and-stick, wire, and space filling model. Central or parallel projection, depth cueing, stereo display.
- Photo-realistic rendered models with user-defined light source and material properties (OpenGL).
- Rotating, shifting, and zooming: mouse-controlled, step-by-step by keyboard, or numerically. Views along specified axes or towards hkl-planes.
- Coordination polyhedral around selected atoms or manually constructed, with hatched, opaque, or transparent faces.
- Display of thermal ellipsoids to visualize anisotropic displacement parameters.
- Labelling of atoms and bonds. Variation of colors, styles and radii of atoms and bonds, either by type or individually assigned.
General:
- 32 Bit MS Windows application with tabbed Multiple Document Interface (MDI), context-sensitive menus, and toolbars. Allows "simultaneous" handling of multiple structures.
- User-defined arrangement of structure picture and diffraction diagram as well as several textual data side-by-side.
- Multiple-step Undo and Redo function.
- Calculation or interactive measuring of distances, angles, and torsion angles, including standard uncertainties.
- Export to crystal and molecular structure formats, peak and |F(hkl)| formats, Windows metafile, several bitmap formats, as well as to Virtual Reality Modelling Language (VRML).
- Online update (automatic or manual).
System requirements
- Personal computer with MS Windows® XP, Vista, Windows 7, Windows 8/8.1 or Windows 10 operating system (does not run on Windows RT or Windows 10 S or Windows 10 in "S mode")
- Microsoft Internet Explorer 5.01 or higher
- 64 MB of RAM
- 100 MB of free disk space
- Graphics resolution of 1024 x 768 pixels with 32,768 colors ("High Color")
