Crysta

Crysta is a crystal workbench that runs in a browser: a single-page tool for crystal structures. Drop in one or more structure files and it expands the symmetry, works out the bonding, sorts the atoms into frameworks, networks and whole molecules, draws the structure in 3D, and lets you measure, label, compare and export. It simulates the powder XRD pattern of each structure and compares it with your measured data. Layered metal halides also get the layer descriptors that 2D perovskite papers use. Nothing is installed and no structure data leaves the browser. The online page counts visits with Google Analytics; the offline file does not.

Crysta grew out of the 2D Perovskite Workbench (this repository was called perovskite-workbench until v0.2.0). What is planned next is in ROADMAP.md.

Use it

• Online: https://wenhao-shao.github.io/Crysta/ (docs/index.html, which loads 3Dmol.js from a CDN).
• Offline: open dist/Crysta.html in any browser. The 3D library is embedded.

Press "Load the sample structures" to load the four built-in samples: (PEA)2PbBr4, (FCA3)2PbBr4 at 294 K (CCDC 2485416), α-quartz and urea. Or drop your own files on the viewer.

File formats

Format	Read	Notes
CIF	yes	symmetry from the listed operators, or from the Hall symbol, H-M symbol or IT number. A file with several data blocks opens as several structures.
SHELX .res, .ins	yes	CELL, LATT, SYMM, SFAC, FVAR, PART; occupancies corrected for site multiplicity
FHI-aims geometry.in	yes	lattice_vector, atom and atom_frac lines. The format has no symmetry. HybriD3 gives some of its structures in this format.
Zip file of the formats above	yes	Each structure file in it opens. From the download of a HybriD3 data set, Crysta opens the CIFs, or the geometry file if there is no CIF. It shows the source and the reference.
VASP POSCAR, CONTCAR, .vasp	yes	version 5 (with the line of element symbols); no symmetry in this format
XYZ, extended XYZ	yes	with Lattice="..." the cell is used; without it the file is shown as a single molecule with no lattice
Powder data .xy, .xye, .csv, .txt, .dat	yes	Two columns of text: 2θ in degrees, then intensity. Crysta ignores header lines. The PXRD window shows the data.
Powder pattern .xy	write	the simulated pattern on its 2θ grid
Powder patterns .csv	write	One 2θ column, then one intensity column for each pattern that the plot shows.
Tripos mol2	write	the shown block, with the cell
PNG	write	1×, 2× or 4× the screen size, optional transparent background
SVG	write	vector drawing of the view; every atom, bond and face is a separate editable object

What it does

• Viewer: ball and stick, space-filling or sticks; atom size and bond width sliders; five element colour schemes; two-tone or gradient bonds; coordination polyhedra; hydrogen bonds; molecule and framework toggles; atom labels; packing limits in cell fractions; views down a cell axis, a [uvw] direction or an (hkl) normal; lattice planes with an offset.
• Measure: click atoms for a distance (two), an angle (three, at the second) or a torsion (four). The picture marks the measured atoms. Remove a measurement with its × in the Measure card or by a right-click on it in the picture.
• Planes: make a plane through three or more atoms, or a lattice plane (hkl) through one atom. Then click one atom for its distance from the plane, two atoms for the angle between their line and the plane, or three atoms for their angle projected onto the plane (Angle in plane). Crysta gives the angle between each two planes, and the lattice plane (hkl) that is nearest to a plane through atoms.
• Polyhedra: automatic around metal centres, and your own: choose a centre element, the corner elements and a distance in the Polyhedra card, or click a centre and a corner in the picture. Press a row to set colour, opacity and edges.
• Element appearance: press an element in the legend to set its colour, size and opacity.
• Structure types: metal-anion frameworks (oxides, sulfides, halides), frameworks joined through molecular linkers, covalent networks, molecular crystals, molecular complexes and salts.
• 2D perovskite module: layer thickness n, spacing, slab and gallery height, in-plane and out-of-plane M-X-M angles, axial tilt, ammonium N penetration, stacking offset. Shown when a layered, halide-bridged framework is found. Press a row of the framework card: its definition shows under the picture, and the atoms and planes of the definition glow in the picture.
• Chromophores: pick three or more atoms on one molecule for a plane and two for an in-plane axis. The definition is copied to every symmetry-equivalent molecule. Each chromophore holds any number of transition-dipole states, drawn as double-headed arrows. 1,2,4,5-tetrazine rings are found automatically.
• Comparison: every loaded structure is a row in one table, which copies to the clipboard as tab-separated text for a spreadsheet.
• Powder XRD: the "Powder XRD" button opens a separate window. Each open structure is a reference: select it to show its simulated pattern. The reflection table gives h k l, d, F, 2θ, I and the multiplicity. Add measured data to compare them with the references, as an overlay or as a stack. Cu Kα1 is the default radiation. Other anodes, a typed wavelength and Kα2 are options. The top axis of the plot gives d in Å. The plot saves as PNG or SVG, the shown patterns as one CSV table, the reflection table as text and the simulated pattern as an .xy file. The arrow at the top right of the reflection table minimizes it, and the plot then has the height.
• Background: the Background menu in the page header sets the whole page to the browser default, to white or to black. The 3D picture, the saved pictures and the PXRD window follow.
• Panels: the arrow at the top right of each card in the rail minimizes or maximizes the card.
• Export: a PNG image of the view, an SVG vector drawing of it, or a mol2 file of the shown atoms.

Feedback

Press "Send feedback" in the page header to report a bug or suggest an improvement. The box offers two routes:

• Send to Wenhao Shao: the note is delivered privately through Formspree, a form service. No account is needed. An optional email address allows a reply.
• Continue on GitHub: the note opens as a pre-filled issue on this repository's Issues page, where you review and submit it with a GitHub account. The issue is public and the email field is left out.

Either way, only the note, the Crysta version and the browser are sent. No structure data is sent.

Definitions

These choices decide the numbers, so they are stated here. Changing any of them needs a version bump.

Quantity	Definition
Covalent bond	two non-metals closer than the sum of Cordero covalent radii plus 0.45 Å
Metal-halide bond	distance below the sum of covalent radii plus 0.75 Å
Metal-donor bond	metal to any other non-metal except H and the noble gases, below the sum of covalent radii plus 0.5 Å; an atom with four or more covalent bonds is not a donor
Polyhedron centre	any metal except Li, Na, K, Rb, Cs, Fr, which are free ions unless they are the only metals with anions around them
Polyhedron	drawn for 4 to 8 bonded neighbours
Polyhedron you define	centre element, corner elements and a largest centre-to-corner distance; drawn for 3 or more corners (3 is a triangle); drawn next to the automatic polyhedra and to other sets, also with the same centre element; changes the picture only
Polyhedron centre in the picture	the centre atom and its bonds are drawn faded inside a polyhedron: 25 % by default, set per row from 0 % (left out) to 100 % (solid); it stays in the mol2 file and in every number
Suggested distance	for each centre the nearest shell ends at the widest relative gap (at least 12 %) among its first 12 sorted distances; the suggestion is the widest shell times 1.08, but at most halfway to the nearest next shell
Covalent network	a set of covalently bonded atoms that a lattice translation joins to itself (diamond, quartz, graphite)
Non-metal polyhedron	B, Si, P, As, S, Se or Te with 4 to 8 bonded neighbours, all of them O, N, F, S, Se, Cl, Br or I; in networks, molecules and molecular ions
Molecular complex	a finite bonded unit that holds a metal and its ligands; drawn whole
Framework dimensionality	number of independent lattice translations that join the bonded network holding the metal centres to itself
Layer spacing	d(hkl) of the layer plane divided by the number of layers per repeat
Layer descriptors	reported for a 2D framework whose bridges between metals are all halides
Layer thickness n	number of distinct metal planes in one slab
Slab thickness	distance along the layer normal between the mean plane of the terminal halides on the top face of one layer and the mean plane of those on its bottom face. It is not a distance between two atoms.
Organic gallery	layer spacing minus slab thickness: the distance from the terminal-halide plane on the top face of one layer to that on the bottom face of the next layer
Δd	(1/6) Σ ((d − d̄)/d̄)² over the six M–X bonds of an octahedron
σ²	(1/11) Σ (θ − 90°)² over the twelve cis X–M–X angles of an octahedron
Octahedron	six neighbours with three trans angles above 150°
θ in	M–X–M angle after projecting onto the layer plane
θ out	M–X–M angle after projecting onto the plane holding M···M and the layer normal
Axial tilt	acute angle between an axial M–X bond and the layer normal
N penetration	depth of an ammonium N below the plane of terminal halides; positive is inside the layer
Stacking offset	in-plane shift between adjacent layers in units of the two in-plane M···M vectors; (½, ½) is ideal Ruddlesden–Popper, (0, 0) ideal Dion–Jacobson
Hydrogen bond	N–H or O–H donor; H···A at least 0.15 Å inside the Bondi van der Waals sum and D–H···A above 120°; acceptors are O and N of another molecule and halide, O, N or S anions
Torsion	−180° to 180°, positive when the far bond is clockwise from the near bond looking down the central bond
Plane through atoms	The least-squares plane through the clicked atoms: it goes through their centroid, and its normal is the direction of least spread. The rms is the root-mean-square distance of these atoms from the plane.
Lattice plane through an atom	The plane through the clicked atom with its normal along the reciprocal vector h a* + k b* + l c*. For a layered structure, the h, k, l boxes start at the (hkl) of the layers.
Atom to plane	The distance of the atom from the plane along the normal, in Å. It is + on the side that the normal points to. For a plane through atoms, the normal follows the order of the clicks.
Bond to plane	The angle between the line through the two atoms and the plane, 0° to 90°. 0° is a line in the plane. 90° minus this value is the angle to the normal.
Plane to plane	The angle between the two normals, 0° to 90°
Angle in plane	The angle A–B–C after both bonds are projected onto the plane: the angle between (A − B) − [(A − B)·n]n and (C − B) − [(C − B)·n]n, with n the unit normal of the plane. 0° to 180°. No value when a bond is within 2° of n. With the layer plane this is θ in.
Nearest lattice plane	For a plane through atoms: the (hkl) with the smallest largest index that is within 1° of the plane. If no plane is that near, the nearest plane with indexes up to 6. Crysta gives the angle between the two planes.
Powder pattern: atoms	Every site and every disorder part, each with its occupancy. Copies of one site that coincide count once.
Scattering factor	Neutral atoms. f0(s) = Σ ai exp(−bi s²) + c with s = sin θ / λ. The coefficients are from International Tables C, table 6.1.1.4. Charges in the file are not used.
Dispersion	f′ and f″ (Cromer–Liberman, as computed by gemmi) for the Kα lines of Cu, Mo, Co, Fe, Cr and Ag. They are zero at any other wavelength.
Displacement	Isotropic: exp(−B s²) with B = 8π²U. The file gives Uiso, Biso or Ueq. Anisotropic values enter as Ueq. An atom with no value gets B = 1 Ų, and you can change that value.
Structure factor	F(hkl) = Σ occupancy × (f0 + f′ + if″) × exp(−B s²) × exp(2πi(hx + ky + lz)), summed over the atoms of the cell.
Reflection set, M	The rotation parts of the space-group operators and Friedel's law make reflections equivalent. M is the number of reflections in the set. Sets with the same d that are not equivalent are separate rows.
Powder intensity	I = M × (mean |F|² of the set) × (1 + cos² 2θ) / (sin² θ cos θ). This factor is for a flat sample in reflection, a beam that is not polarised, and no monochromator. The strongest reflection in the 2θ range is 100.
|F| in the table	The root of the mean |F|² of the set. F (real) and F (imaginary) are for the reflection that the row names.
Peak shape	Pseudo-Voigt with one width at every angle. The defaults are FWHM 0.1° and Lorentzian part 0.5. The area of a peak is its I. The highest point of the pattern is 100.
Second wavelength	Every reflection occurs again at the angle of λ2. Its intensity is I × the intensity ratio × the ratio of the two Lorentz-polarisation factors.
Measured data	Crysta scales each data set so that its highest point in the 2θ range is 100. It subtracts nothing. It adds the 2θ shift to every point.
d axis of the PXRD plot	d = λ1 / (2 sin θ), for the first wavelength only.
CSV of the PXRD plot	The 2θ column is the grid of the Pattern settings, for the full range. The values are as plotted. Crysta puts measured data on the grid by linear interpolation between the two nearest points.
mol2 atom types	SYBYL types guessed from the element and the number of bonded neighbours; every bond written as single
SVG drawing	the screen view without perspective; objects written back to front by the depth of their centre; of each polyhedron only the faces turned to the viewer

Disorder

• Flagged parts: within each disorder assembly the group with the highest mean occupancy is shown.
• Unflagged split sites: two non-H atoms of one element closer than 0.9 Å are treated as alternates and the first listed is shown.
• Negative part numbers (disorder over a symmetry element): one orientation is kept.
• All geometry is computed on the shown component. The formula and density use every part, weighted by occupancy.
• A file that holds a single component and no flags is treated as ordered.

Known limits

• Bonds between two metals are not drawn, so elements and alloys appear as separate atoms.
• H is never taken as a ligand of a metal, so hydrides show no M–H bonds.
• A-site ions other than the alkali metals (Ba, Sr, La in oxide perovskites) are treated as bonded centres; with more than 8 neighbours they get bonds but no polyhedron.
• The non-perovskite structure classes are tested on constructed files with literature cell and coordinates, not yet on a set of deposited structures.
• SHELX, POSCAR and XYZ reading is tested on one small file each.
• Quasi-2D (n > 1) and symbol-only paths are tested on constructed files only.
• There is no way yet to choose a disorder component other than the major one.
• A chromophore follows crystallographic sites, so a structure with two independent cations needs one definition per cation.
• The stacking-offset and tilt descriptors assume corner-sharing layers.
• Polyhedra you define use one distance for all their corner elements, and are not kept after the page is closed.
• Appearance is set per element, not per atom or per site, and is not kept after the page is closed.
• An element drawn see-through keeps solid bonds.
• The mol2 file carries no bond orders or charges.
• The powder pattern has no preferred orientation, no absorption, no background and no instrument function. The peak width is the same at every angle.
• Crysta has f′ and f″ for six anodes only. It treats ions as neutral atoms. It simulates X-rays only.
• A structure file without symmetry (POSCAR, XYZ with a lattice) lists reflections that are equivalent in the real symmetry as separate rows.
• For a large cell the simulated 2θ range is cut, and the PXRD window says where.
• Crysta reads measured data from text columns only. It does not read Bruker .raw or .brml files, or PANalytical .xrdml files. It does not fit the simulated pattern to the data.
• The PXRD window belongs to the Crysta page that opened it. It closes when that page closes. Patterns and data are not kept after that.
• The page does not remember the minimized cards after it closes. It does remember the Background choice.
• The CSV of the PXRD plot holds measured data after interpolation, not the measured points. Use a step that is not larger than the step of the measurement.
• The SVG drawing sorts whole objects by depth, so objects that pass through each other (a bond through a polyhedron face, crossing lattice planes) can overlap in the wrong order. It has no perspective and no lighting beyond the shaded atom fill.

Develop

python3 build.py      # writes docs/index.html and dist/Crysta.html
node tests/run.js     # regression tests for src/core.js

• src/core.js: file reading, symmetry, bonding, geometry, powder diffraction, mol2 and SVG writers. Pure functions, no DOM, runs in Node.
• src/workbench.template.html: the page and its interface code.
• src/pxrd.js: the PXRD window (plot, reflection table, measured data). It gets its numbers from core.js.
• src/dbs.js: the Databases window. design/ holds the design notes.
• tools/hybrid3_copy.py: copies the HybriD3 entry list and the list of its structure data sets into data/hybrid3/. It keeps no structure file. The job .github/workflows/hybrid3-copy.yml runs it by hand. build.py puts the lists into the page.
• src/sg-table.json: Hermann–Mauguin symbol to Hall symbol, for CIFs that list no operators.
• examples/: the CIFs embedded as built-in samples. The reflection list was removed from the (FCA3)2PbBr4 file (CCDC 2485416) to keep the page small, and its CCDC number was added as a data item. The quartz and urea files were written for Crysta from literature values.
• tests/: regression tests, including operator lists for every tabulated Hall symbol, one small structure per crystal class in tests/cifs/, and one file per extra format in tests/files/.
• vendor/: 3Dmol.js 2.5.5 (BSD-3-Clause) for the offline build.

The name and version live in package.json (displayName, version) and are printed in the page.

How to cite

Crysta has no paper and no DOI yet. Cite it as software, with the version:

W. Shao, Crysta: a crystal structure workbench in the browser, version 0.5.0 (2026). https://wenhao-shao.github.io/Crysta/

• The "How to cite" button in the page gives this citation for the version that you use, also as BibTeX.
• CITATION.cff has the same data for GitHub and for reference managers. build.py makes it from the "citation" part of package.json: change the authors, the title and the release date there.
• Cite also the source of each structure file, and 3Dmol.js for the pictures (N. Rego and D. Koes, Bioinformatics 31, 1322–1324 (2015)).

Licence

MIT. See LICENSE. 3Dmol.js is distributed under its own BSD-3-Clause licence, see vendor/.