Technical Specifications

Molecule Builder

• Click with the Add Atom tool to define the positions of new atoms. Shift-click to simultaneously add an atom and a bond.
• Atom Picker palette lets you change the atom type associate with the Add Atom tool.
• Selection menu provides commands to duplicate, detach, move or edit any group of selected atoms.
• Use the Relax Molecule command to optimize your molecule, via a sophisticated Monte-Carlo algorithm that takes into account the existing bonding, and auto-identifies carbon hydridisation.
• Option to relax a selected group of atoms, independently of the rest of the structure: ideal for working with extended, macro-molecular structures.
• Add Hydrogens command. Provides energy minimization for new H positions, leaving the remainder of the molecule unchanged - hence ideal for adding H atoms to an "X-Ray Structure".

Energy Modelling

• Force field approach, using parameterised potentials (MM3 where possible, otherwise UFF).
• Smart selection of potentials, based on bonding environment: requires no additional user input.
• Monte Carlo technique allows relaxation of structures far from equilibrium - e.g., crude, hand-drawn structures with excessive bond lengths and distorted bond angles!
• Hybrid least-squares cycle added to provide greater precision in the closing stages of refinement.
• Uses the best-available MM3 potentials, falling back onto UFF (Universal Force Field) where necessary. (Parameterised potentials calibrated using DFT, for greater accuracy.)
• Provides energy output, available in graphical form during the course of the refinement cycle, and later, via a menu command.
• Calculates vibrational modes, including frequencies and simulated infra-red spectrum, plus interative visualizations of vibrations in the Vibrations Explorer.

Crystal Building

• Build any crystal structure, using the Crystal Editor: spacegroup, unit cell parameters plus asymmetric unit.
• Unlimited numbers of chemical occupants per site - e.g., to allow for subsitutional disorder. Formula input can be used (e.g., "T1" with Al 0.75 Si 0.25), without requiring use of duplicate mono-atomic sites (e.g., one "T1" with Al 0.75; second overlapping "T1" with Si 0.25).
• Accepts coordinates as decimals or fractions, with automatic syntax checking.
• Accepts atomic displacement parameters as isotropic parameter (U_iso), or anisotropic (U_ij). (B_ij values are used internally, and can be read from text files.)

Symmetry Handling

• Auto-recognition of short and full international spacegroup symbols for all 230 conventional spacegroups, plus all alternate settings listed in the International Tables for Crystallography
• Auto-recognition of Schoenflies symbols and/or spacegroup numbers
• Symmetry Explorer allows easy navigation through crystal systems, lattice types and spacegroups, with optional display of unconventional settings and detailed spacegroup information. Spacegroups can be searched, by number, short or full international symbols, or using Schoenflies symbols.
• Symmetry Browsing allows editing of lattice types, general equivalent positions and origin offsets
• Automatic definition of symmetry-constrained lattice parameters (Constrain lattice parameter option)
• Automatic spacegroup detection when loading text files. Provides spacegroup symbol display in the Edit > Structure dialog, and in file output.

Plot Range

• Hide atoms by site, element, or individual selection
• Customize atom visibilities by hiding or isolating groups of atoms
• Spherical ("cluster") display option with real-time radius control
• Crystal Plot Range popover: real-time control over xyz plot range

Atom Colours and Radii

• Atoms can be coloured by default (element type), by site, or individually (by selection).
• Atom styles (spheres or ellipsoid styles) can be applied on a per-element, per-site, or per-atom basis (e.g., using the Selection Inspector).
• Wide range of styles, including photo rendered spheres, two-tone, beach ball, translucent - plus numerous stylized variants include square (vacancy), emoji (happy/sad), dotted, dashed, stripe-fill, etc.
• User-defined sphere radii, including control over ball-and-stick spheres.
• Automatic recognition of element symbols, matching current global element table: defines colours and radii.
• Atoms Inspector allows switching between custom and pre-set tables of element radii (e.g., Van-der-Waals, Atomic, Ionic, Covalent)
• Elements pane of the Preferences Panel provides editing of global element specifications, plus import/export of atom colour/radius values.
• Shannon & Prewitt "crystal radii" are used by default, but can be changed to any of the preset element tables using the Preferences Panel.

Thermal Ellipsoids

• Wide range of 3D (photo-rendered) and 2D (stylized) ellipsoid styles, including solid, octant-cut, translucent (with or without axes), equatorial markings, etc.
• Option to display individual sites or elements as small spheres instead of ellipsoid.
• User-defined thermal ellipsoid probability value with option of plotting selected sites as spheres of an arbitrary size (e.g., H atoms).

Bonding

• Auto-Generate Bonds option
• List Bonds command - provides bond searches and full, concise, or histogram output around specified sites
• Distance Explorer provides a graphical summary of distances in the structure between specified sites and/or element combinations
• Bonds Inspector allows control over individual bond specifications, including minimum and maximum distances for bonding between pairs of chemical elements.
• Primary and Secondary bonds can be defined - the latter are assumed to be inter-molecular bonds
• Multiple bond specifications for the same element pairs make it possible to distinguish covalent from hydrogen bonding (e.g., H--O versus H...O).
• Wide range of bonds styles including cylinder, double & triple bond, dashed, dotted, banded, two-tone styles. Can be applied globally (i.e., as a property of a bond specification), or locally (to one or more selected bonds)
• Choice of thick or thin cylinder styles; exact radius dependent on minimum sphere radius; can be customized in the Model Inspector.
• User-defined relative bond radii for ball-and-stick and stick model types.

Polyhedra

• Automatic generation of polyhedra, following bond generation.
• Extensive choice of polyhedral styles including solid, translucent and hybrid styles (with ball-and-stick/vertex atom).
• Assign polyhedral styles on a per-element, per-site or per-atom basis, using popover windows in the Atoms Inspector or Selection Inspector.
• Option to display thermal ellipsoids (or atoms spheres) at vertices.
• Option of Convex or concave polyhedra generation.
• Curved faces display option for concave polyhedra (ideal for MOFs).

Preset Model Types

• Ball-and-stick
• Stick
• Space filling
• Wire frame
• Thermal Ellipsoids
• Polyhedral - including combinations of the other model types (e.g., polyhedra with ellipsoids at the vertices)

Unit Cell Display

• Display single, or multiple unit cells.
• Solid, dashed or dotted line styles with user-defined pen width and colour.
• Emphasize Front Edges options: enhances the 3D impression by differentiating visible and hidden edges.
• Translucent or opaque fill for cell faces.

Surface Overlay

• Space-Filling, Van-der-Waals or Solvent-Excluded surface (with customizable probe-sphere radius).
• User-defined colour & opacity

Lattice Planes

• Multiple lattice planes in any orientation - including automatic generation of symmetry-related planes.
• Display of parallel sets of planes.
• Real-time control of plane position, via slider control.
• Buttons to move planes to hkl intercepts, or to model centre

Volumetric Data

• Visualize multiple periodic 3D datasets in the same window - with or without your crystal structure model.
• Imports: 3ED, CASTEP, Gaussian CUBE, DEN, GRD, GULP, VASP, Voxel and XSF file formats.
• Iso-surfaces and iso-volumes, with gradient display or customizable interior, exterior and truncation colours.
• Point clouds, with variable size or colour gradient.
• (Multiple) lattice-plane slices, with variable translucency.
• Control data range interactively, with the Range slider and its histogram preview. An optional interval lock lets you rapidly browse iso-volumes at different threshold values.
• Specify range limits using absolute or relative units.
• Mode, Median, Middle, Mid-Range, Full-Range presets
• Bicubic interpolation (oversampling) for sparse datasets.

Atom Vectors

• Vectors can be added to any selected atom, in user-specfied orientations [UVW], colour and length.
• Choice of "From Atom" or "Through Atom" (William Tell) styles
• Selected vectors can be edited en masse, including setting the orientation and style.
• Multiple vectors can be imported from text data (CMTX files), e.g., for visualization of vector fields.

Annotation

• Atom labels: element type, site, or for individually-selected atoms. Choice of global site labels, chemical element, atom numbers or z-coordinate display, with user-defined font and positional settings.
• Bond labels (distance)
• Overlay text boxes, with rich-text content, including superscripts and subscripts.
• Lines and arrow overlays

Model Extras

• Display of "xyz" or "abc" axial vectors in any corner of the screen, or the centre.
• Legend display: with or without a border or translucent fill; can be dragged to different parts of the screen.
• Customizable background colour, gradient fill and/or background picture (imported from a graphics file)

Rendering Options

• Phong rendering model, with full control over ambient, diffuse and specular reflection from atom spheres, bonds, polyhedra and surfaces
• Up to 5 light sources (ambient plus 4 spotlights), with real-time adjustment via sliders, multi-touch stereograms and bearing/elevation controls. Includes backlighting option.
• Polyhedral frame highlight option: subtle, light, dark (with custom thickness)
• Depth Fading - control and extent
• Depth Profiling with real-time zoom control (Mac)
• Translucency supported for all model types - CrystalMaker does this "properly", compared to other programs, with correct overlaps and fading.
• Live adjustment of Perspective view distance.
• Stereo-pair plots, with control over image separation and +/- angular separation.
• Red/blue stereo with stereo standout and angular separation options.

Molecular Crystal Tools

• Show Molecular Unit: the fastest way to show one or more intact molecules.
• Show Asymmetric Unit.
• Show Molecular Cell: complete unit cell contents with fully-intact molecules.
• Repair "broken" molecules.
• Hide Stranded (underbonded) atoms
• Hide Molecular Fragments.
• Repair Molecular Fragments.
• Extend selection to entire molecule.
• Isolate molecule (hide any molecules with unselected atoms).

Selection Tools

• Shift-click with Arrow tool to select groups of atoms.
• Click-and-drag with Arrow tool to define rectangular selection.
• Lasso tool.
• Polygon tool.
• Extend selection to nearest neighbours (with or without bonds selected). This can be repeated iteratively to grow a selection.
• Extend selection to an entire ring.
• Extend selection to molecular fragment(s) containing one or more selected atoms.
• Extend selection to entire molecule(s) containing one or more selected atoms.
• Selection of symmetry-related atoms or bonds.
• Isolate or hide a selection.

Interactive Measurement

• Screen ruler and Screen distance tool
• Arrow tool provides "rollover" with atom identification and bond labelling.
• Selection Inspector displays extended atom/coordination/bonding information.
• Bond Distance tool with rollover mode (anchor the first atom; rollover other atoms as the distances are updated).
• Bond Angle tool with rollover mode (anchor the first two atoms; rollover other atoms as the angle is updated).
• Torsion Angle tool with rollover mode.

Calculation

• Porosity.
• Porosity maps: visualize negative (void space) or positive (filled space).
• Electron density maps: crystal simulation using built-in atomic scattering factors and visualization as point clouds, lattice plane slices, iso-volumes or iso-surfaces.
• Distance maps: ideal for visualizing cavities and channels.
• Van der Waals surface.
• Solvent-Excluded surface - with real-time control over the probe radius.
• Cavity Finder. Option to automatically add correctly-sized cavity centroids as translucent spheres.
• Centre-of-gravity of selected atoms, with distances to centre
• Distance Explorer with atomic distance number/density graphs.
• Pair Distribution Functions (x-ray and neutron) with optional Partial P.D.F. display.
• Nearest-neighbour bond searches: user-specified search distance from specified sites. Choice of detailed, concise, or histogram display in the Output pane of the Overview window.
• Bond distances - with full error propagation (where relevant).
• Distance from selected atom(s) to a displayed lattice plane
• Angles between specified lattice vectors and/or lattice plane normals (Calculate Angle dialog)
• Angles between any displayed lattice planes
• Angles between molecules
• D-Spacing.
• Distance between any two parallel planes.
• Best-fit line or plane through selected atoms.
• Unit cell volume.
• Polyhedral volumes.
• Density.
• Chemical formula.
• Energy (for a molecular system).
• Vibrational Modes (for a molecular system) - with optional output including eigenvectors and eigenvalues.
• Infra-Red Spectrum (for a molecular system) - with extensive customization of axes (absorbance, transmittances, increasing/decreasing x) and graphics display.
• Ring topologies around any selected atom.
• Cavity Finder: automatically locates any cavities in your crystal above a minimum specified size. Optionally adds a correctly-sized, translucent sphere, at each cavity location.
• Molecular Centroids: simplifies complex molecular crystals by representing the centre of each individual molecule by a single (dummy) site.

Manipulation

• Multi-touch: pinch-to-zoom, rotate; use a two-finger swipe gesture to rotate about horizontal (X) or vertical (Y) axes.
• Touch Bar rotation and zoom controls (MacBook Pro)
• Haptic feedback on all screen tools (requires a Mac with a force-touch trackpad).
• Leap Motion 3D hand gesture control (Windows): supports one-handed (3-axis) or two-handed (rotation + scaling) control with the Leap Motion Controller (Windows version only).
• Mouse-driven structure rotation
• Mouse wheel support for x, y and z rotation (via keyboard modifiers)
• Accelerated rotation option
• Toolbar rotator pad for rotation through precise angle steps
• Auto Rotate command, provides controlled rotation through pre-controlled rotation sequences, including "jiggle-mode" and continuous rotation.
• Toolbar scale buttons, with accelerated scale option (shift key down).
• User-defined scale (dialog entry).
• Mouse-driven movement of entire structure (Move tool).
• Mouse-driven movement and rotation of individually-selected atoms (Arrow tool).
• View down any lattice vector or plane normal (Set View Direction command).
• Playback controls including Animation Scrubber for fast scans of multi-structure sequences and simulation trajectories.

Touch Bar Interfaces (MacBook Pro)

• Library
• XYZ Rotation dials
• Preset view directions
• Zoom, auto scale, auto centre
• Atom picker
• Animation scrubber
• Spin
• Vibrational mode picker & scrubber

Transformation

• Option to repair a selected coordination environment ("repair nearest neighbours").
• Merge two-or-more selected sites into a single site (e.g., for a disordered structure).
• Merge multiple structures into a single crystal or molecule.
• Transform Crystal to Molecule (and vice versa) option
• Lattice transformations: using a 3×3 transformation matrix to convert the unit cell (basis) vectors; pre-set conversions for common operations, e.g., hexagonal to primitive (rhombohedral axes).
• Supercell generation (and collapse)
• Visualize disordered sites: transforms a structure with "average" atoms into a supercell with randomly distributed elements/vacancies for any disordered sites (e.g., Cu_0.5Zn_0.5).
• Lattice plane projections. Project the unit cell onto the lattice plane of interest, to create a new "surface cell".
• Moveable origin. Specify a new origin in the structure, or select one or more atoms and use the centroid.

Crystal Engineering

• Combine multiple structures into the same window, e.g., to visualize domains or interfaces.
• Insert a space in a crystal lattice, parallel to a lattice plane, with specified width.
• Insert new atoms into the unit cell, using the Add Atom tool.
• Duplicate atoms inside the unit cell.
• Directly edit the coordinates and/or offsets of any selected atoms.
• Move selected atoms with the mouse or keyboard commands.
• Change atom type for any selected atom.
• Visualize disordered sites via smart supercell generation and element-type reasignment.

Graphics & Video

• 3D Printing Support. Export self-contained 3D models suitable for printing, in the STL 3D (binary) file format.
• COLLADA 3D output. Provides a handy interchange format, for conversion to third-party 3D formats. Works with Apple iBooks Author, to provide self-contained, fully-rotatable 3D images for use in iBooks on the iPad or Mac.
• High-resolution graphics copied to the clipboard.
• Vector graphics export to PDF or EPS (Mac), or WMF (Windows).
• Photo-realistic pixel-rendered TIFF, JPEG, BMP, PNG, (user-specified size and resolution) - with option of transparent backgrounds (PNG and TIFF).
• High-resolution printing
• Save animations as videos, with option of loop back-and-forth. H.264 output in QuickTime (Mac) or AVI (Windows).
• Automatic generation of rotating-structure movies, with user-defined rotation steps, rotation speed, looping, etc.

Window Options

• Multiple windows can be opened and organised using Tile and Stack commands.
• Works with Full Screen mode and "Spaces" (Mac)
• Document tabs (macOS Sierra or later)
• Multiple structures in the same window, shown as thumbnails in the Structures List.
• Drag-and-drop structures between windows

Program Limits

(subject to system RAM)

• Unlimited numbers of atoms, bonds and polyhedra.
• Unlimited polyhedra sizes.
• Unlimited number of structures per window.
• Unlimited undo/redo levels (size of undo buffer can be constrained in the Preferences Panel).

Structure Import/Export

CrystalMaker provides automatic drag-and-drop import of over 40 different file formats - based on standarized file extensions or, in some cases, filenames (e.g., "HISTORY" for a DL_POLY file). Automatic format recognition can be overriden using the File > Open File with Format command.

	Format	Import	Export
1.	3ED	•
2.	ATOMS	•
3.	CASTEP Cell	•	•
4.	CASTEP Output	•
5.	CASTEP Volumetric	•
6.	CCL	•
7.	Chem3D Cartesian	•	•
8.	CIFa	•	•
9.	CMDF	•
10.	CMDX	•	•
11.	CMMF	•
12.	CMTX	•	•
13.	CSSR	•
14.	Gaussian CUBE	•
15.	DEN (Volumetric)	•
16.	DL_POLY Config	•
17.	DL_POLY Revcon	•
18.	DL_POLY History	•
19.	DMol3 ".car"	•	•
20.	DMol3 ".arc"	•
21.	FDAT (CSD)	•
22.	GRD (Volumetric)	•	•
23.	GROMACS	•
24.	GSAS	•
25.	GULP	•
26.	ICSD	•
27.	LAMMPS	•
28.	Molfile	•
29.	PDB	•	•
30.	RMCProfile	•	•
31.	SDfile	•
32.	SHELXb	•
33.	STRUPLO	•
34.	SYSTREC	•
35.	TOPAS	•
36.	VASP Structure	•
37.	VASP Trajectory	•
38.	VASP Volumetric	•
39.	VESTA	•
40.	Voxel	•	•
41.	WIEN2k	•	•
42.	XCrySDen Structure	•
43.	XCrySDen Animation	•
44.	XYZ	•	•

Import Notes.

a. CIF: Imports multiple structures from a single CIF file, including thermal and error parameters (where available).

b. SHELX: Supports multi-part SHELX files, with the option to display a composite structure or individual states of the disordered model.

c. SYSTRE: Automatic colour-coordinated display of symmetry-related bonding.

Other Data Formats

	Format	Import	Export
1.	Elements	•	•
2.	Coordinates		•
3.	Visible Coordination		•
4.	Crystal Coordination		•
5.	HTML Structure		•
6.	Distances & Angles		•
7.	Vibrations List		•

Structures Library

CrystalMaker includes an integrated library browser/viewer with examples, reference structures and teaching resources. The library includes quick links to documentation, recently-opened files and allows you to add your own structures (and organise) the "Favourites" collection. The library's permanent collections include:-

• Examples: a series of annotated structures designed to showcase the program's capabilities.
• Reference: over 1,200 structures subdivided into: Hybrid Structures (MOFs, ZIFs, Clathrates), Organics and Inorganics (including over 400 rock-forming minerals).
• Teaching: annotated structures designed to be used "out of the box" in teaching exercises. Includes: Atomic Radii (Periodic Tables of the elements with ionic, covalent, Van-der-Waals radii), Basic Structure Types (crystal-chemical "type" structures), Crystalline Elements, Lattice Types, Polyhedra, Structural Architecture (multi-structure documents designed as self-running animations to explain complex structures in terms of simple building bricks).
• Thematic: a selection of newsworthy structures, organised by topic. Includes Food, Fuel, Medicines, Narcotics (and various other nasties).

A powerful search command lets you quickly find structures by name, notes or chemical composition. An integrated CrystalViewer offers rotatable previews and animations, with full textural descriptions.

Please don't confuse this with the usual dusty database! This is a carefully-curated exhibition of the material world, with engaging, colourful structural models that are annotated (often with multiple views) and ready for instant display.

Support Options

CrystalMaker comes with full-featured technical support, starting with support resources shipped with the program (online help and an illustrated PDF user's guide), and including first-class technical support eligibility for registered users.

• Comprehensive online help system, with index, accessed via context-sensitive help buttons or menu commands.
• Deluxe, 400-page user's guide, in full colour, searchable PDF format.
• Two tutorials, in PDF format.
• Online Video Tours.
• Online Video Tutorials.
• Online Advice Centre.
• First-class technical support for registered users, for the lifetime of the product (defined as being the interval between one first-digit version upgrade, and the next).