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Keep the cubic translations above, but attach an atomic basis with A at fractional crystal coordinates $(0,0,0)$ and B at $(u,0,0)$. Stipulate real, angle-independent relative scattering amplitudes $f_A=1$ and $f_B=0.6$. Neglect wave absorption, repeated crystal scattering and thermal motion. This is a point-scatterer model under the Born approximation, not a claim about the scattering strengths of named elements. Its crystal basis structure factor isHere $J$ is a dimensionless squared motif amplitude. Comparing it with measured integrated wave intensities requires the experimental geometry and detector response as well. The algebra follows directly by multiplying $F$ by its complex conjugate; the cross term records wave interference between the two sites.

With $u=1/2$, reflections with even $h$ have $J=2.56$, whereas odd $h$ gives $J=0.16$, a ratio of $16:1$. With $u=1/4$, the first four $(h00)$ values instead are $1.36,0.16,1.36,2.56$. Their geometrically possible positions are unchanged, although their strengths change. For equal stipulated amplitudes $f_A=f_B=1$ and $u=1/2$, the odd-$h$ amplitude vanishes exactly: an example of a systematic absence. Different motif weights can thus expose a repeat that equal weights conceal.

The same formula also proves an ambiguity: $u=1/4$ and $u=3/4$ give identical $J_{hkl}$ for every integer $h,k,l$, because $\cos (2\pi h(1-u))=\cos (2\pi hu)$. Yet $F_{100}$ changes from $1+0.6i$ to $1-0.6i$, reversing its wave phase. This particular ambiguity is inversion of the motif; it does not prove that these two simple motifs are distinct chemical substances. The conclusion is conditional on the stipulated real scattering amplitudes.

Fractional crystal coordinates are the dimensionless coefficients in $r=u{a}_1+v{a}_2+w{a}_3$ for specified unit cell vectors. They are not Cartesian lengths unless the vectors themselves are included. With primitive vectors, replacing $u,v,w$ by values differing by integers selects an equivalent position in another unit cell.

In the two-dimensional example under crystal structure, B has position $(0.65,0.55)$ in ordinary length coordinates, but fractional crystal coordinates $(0.65/2,0.55/1.5)=(13/40,11/30)$. Multiplying these coefficients by the two translation vectors recovers the drawn position. Reporting the axes is therefore part of reporting a structure.

The phase problem is the loss of the wave phases of the crystal basis structure factors when an experiment records their squared magnitudes. Write $F_{hkl}=|F_{hkl}|e^{i{\varphi }_{hkl}}$. A Fourier series reconstruction of a periodic electron density uses both $|F_{hkl}|$ and ${\varphi }_{hkl}$, whereas an ordinary wave intensity measurement supplies only $|F_{hkl}{|}^2$. Estimating the missing phases therefore needs additional constraints or measurements.^[ref]

There is also an unavoidable choice of origin. Translating all motif positions by the same fractional crystal coordinate vector $t$ multiplies $F_{hkl}$ by $e^{2\pi i(h,k,l)\cdot t}$ without changing $|F_{hkl}{|}^2$. The physical arrangement is unchanged. A reconstructed coordinate list must therefore distinguish a coordinate convention from information actually recovered from the measurements.