Paste any crystallography output and find out whether your crystal is a known structure already in the PDB.
What to paste
XDS CORRECT.LP, Aimless / Scala log, HKL2000 output, CCP4i summary, beamline log, or a bare CRYST1 line. The parser extracts the unit cell and space group automatically from whatever you paste.
How matching works
Your cell and every PDB X-ray entry are Niggli-reduced (canonical form with a ≤ b ≤ c) before comparison. This makes matching robust to different conventional settings and surfaces missed or added symmetry automatically — the metric is compared without regard to the space group.
Result badges
Identical — same space group as your query
Enantiomorph — mirror-image SG (one of 11 Sohncke pairs); same structure, opposite hand
Missed / added symmetry — same point group, different screws; may be over- or under-symmetrised
Same system — same crystal system; possible sub/supergroup or pseudosymmetry
Check pseudosymmetry — unrelated SG, similar cell metric; check for NCS or twinning
Distance Δ
Normalized RMS over the 6 Niggli-reduced parameters: lengths as fractional deviation, angles divided by 90°. 0 = identical; ~0.015 ≈ the default tolerance boundary. Hover the Δ value on any hit for the formula.
Background
Nearest-cell (Ramraj et al., 2012, Acta Cryst D) pioneered PDB cell lookup but is no longer available. It reduced cells to P1 and tested all six axis permutations via MATFIT rotation superposition. Déjà Vu takes the same idea further: Niggli reduction gives a unique canonical form directly — no permutation enumeration — and every hit is labelled with its space-group relationship rather than just a distance.
Data
All X-ray entries from the RCSB PDB. Index refreshed weekly; release date shown in the footer. Hover any ? badge in the interface for field-specific explanations.
DéjàVuv1
Paste your unit cell & space group — find out if you’ve re-crystallised a known structure
Paste crystallography output
Unit cell
Space group
Symbol—
Number—
System—
Z—
Advanced parameters
Cell tolerances
Length±1.5 %?
Angle±1.5°?
Show relationships
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?
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Mission statement & references
DéjàVu
is a modern replacement for
Nearest-cell
(Ramraj et al., 2012), which is no longer available.
Collecting data from a crystal that’s already in the PDB wastes beamtime —
this tool catches that before you commit to a full dataset.
Both your cell and the entire PDB X-ray index are compared in
Niggli-reduced form (canonical a ≤ b ≤ c),
making the search robust to axis reordering, missed symmetry, and enantiomorphic
settings, with every hit labelled by its space-group relationship to your query.
Nearest-cell reduced to P1 and tested all six axis permutations via MATFIT rotation
superposition; Niggli reduction gives a unique canonical form directly —
no enumeration needed.
I wanted a fast, browser-accessible alternative — no original crystallographic
science was performed by me.
— Jan Gebauer
References
Ramraj, A., Evans, G., Diprose, J.M. & Esnouf, R.M. (2012)
Nearest-cell: a tool for the identification of similar unit cells.
Acta Cryst.D68, 1697–1700.
doi:10.1107/S0907444912039047
Křivý, I. & Gruber, B. (1976) A unified algorithm for determining the
reduced (Niggli) cell. Acta Cryst.A32, 297–298.
doi:10.1107/S0567739476000636
Grosse-Kunstleve, R.W., Sauter, N.K. & Adams, P.D. (2004)
Numerically stable algorithms for the computation of reduced unit cells.
Acta Cryst.A60, 1–6.
doi:10.1107/S010876730302186X
Paste a unit cell & space group above, then press Search.