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STEMORIA scientific instrument
Compare ordered XYZ coordinate sets across raw, translation-only, and equal-weight proper-rigid RMSD while inspecting the corresponding 3D transform.
01
Manipulate
02
Measure
03
Interpret
Scientific viewport
Spatial reasoning engine
Compare two structures imported through the same authoritative format adapter at raw, translation-only, and equal-weight proper-rigid alignment levels.
Original source coordinates
Structure A · reference
Display fitting is representation-only and does not change comparison coordinates.
Structure B · source
The source geometry is shown before any scientific alignment transform.
Comparison ladder
Format
Points
Raw RMSD
Translation-only RMSD
Proper-rigid RMSD
Centroid shift
Rotation determinant
Per-point displacement
| Point | Raw | Translation only | Proper rigid |
|---|---|---|---|
| 1 | 2.44949 | 0 | 0 |
| 2 | 1.41421 | 2 | 4.96507e-16 |
| 3 | 3.74166 | 2 | 4.96507e-16 |
| 4 | 2.44949 | 2 | 2.22045e-16 |
| 5 | 4.24264 | 2 | 2.22045e-16 |
Rigid transform
Rotation matrix
[-2.22045e-16, 1, 0]
[-1, -2.22045e-16, 0]
[0, 0, 1]
Translation
[-1, 2, 1] coordinate units
Alignment source
Berthold K. P. Horn / Journal of the Optical Society of America A
Closed-form solution of absolute orientation using unit quaternions (1987), DOI 10.1364/JOSAA.4.000629.
Scientific boundary
Both sides must use the same import format in this v1 so coordinate semantics are not mixed silently. XYZ units are user-declared; PDB coordinates are Å; SDF V2000 coordinates remain CTfile coordinate units without a physical-unit assumption.
Point correspondence remains positional after import: same point count, same order, and matching labels are required. PDB alternate locations are selected explicitly for each side.
Proper-rigid alignment uses equal weights, translation, and a proper rotation only. No reflection, atom permutation, graph matching, symmetry matching, mass weighting, flexible fitting, or periodic-boundary handling is performed.