Is the ‘Geometric Centre’ the centre of mass?

No. It is the arithmetic mean of the atomic coordinates (a geometric centroid). A true centre of mass would weight each atom by its atomic mass.

Does translation distort my molecule?

No. Rigid-body translation and centring shift every atom by the same vector, so all internal distances and angles are preserved.

Coordinate Manipulator

Translate, rotate and re-box PDB, GRO and XYZ coordinates in the browser; nothing is uploaded.

Or try a sample:

PDBENTGROXYZ

structure.pdb

System statistics

Atoms: 0
Geometric centre: 0.0, 0.0, 0.0
Centre of mass: 0.0, 0.0, 0.0
Molecular weight: —
Bounding box: 0.0 × 0.0 × 0.0

How the mass was calculated

Sum of standard atomic weights over every atom present in the file, including solvent and ions. Natural-isotope averages, not monoisotopic masses; no charge correction.

Translation

Adds this vector to every atom; the unit follows the source file.

x (Å)

y (Å)

z (Å)

Centre using

Rotation

degrees

Applied as intrinsic Z‑Y‑X (yaw, then pitch, then roll) about the pivot below. Rigid rotation, bond lengths and angles are preserved.

x (°)

y (°)

z (°)

Rotate about

Simulation box

Written to .gro output and as CRYST1 in PDB. GROMACS always expects nanometres here, whatever the source file used.

Lx (nm)

Ly (nm)

Lz (nm)

Padding (%)

Export

Format

File name

Writes translated_sys.xyz.

Equivalent gmx editconf command

Load a structure to see the equivalent command.

Output buffer XYZ

How to translate and convert molecular coordinates

Shift a structure by a vector, centre it on the origin, or convert between PDB, GRO and XYZ (with correct unit handling) without installing anything.

Load a structure

Drag & drop (or click to browse) a .pdb, .gro or .xyz file. Parsing starts automatically.

Inspect the system

Read off the atom count, geometric centre and bounding box, all shown in the file’s native units (Å for PDB/XYZ, nm for GRO).

Transform

Apply a translation vector, rotate about any axis in degrees, or press Align Origin to move either the geometric centre or the true centre of mass to (0, 0, 0).

Export

Choose an output format and click Download. Coordinates are converted to the correct units for the target format automatically.

How the coordinate manipulator works

Units are handled for you

PDB and XYZ files store coordinates in ångström (Å); GROMACS .gro files use nanometres (nm), where 1 nm = 10 Å. The tool keeps atoms in the source unit for display and transforms, then converts on export, so a .gro loaded in nm is written out as a valid .pdb in Å. Every input label updates to show the unit currently in force, so there is nothing to remember.

Geometric centre vs centre of mass

The geometric centre is the unweighted mean of the coordinates, every atom counts equally. The centre of mass weights each atom by its standard atomic weight, so heavy atoms pull it toward them. For a water molecule the two differ by roughly 0.28 Å. Both are shown live, and either can be moved to the origin.

Rigid-body operations

Translation adds a constant vector to every atom. Rotation applies an orthogonal matrix about a pivot you choose. Both are rigid: all bond lengths and angles are preserved, verified here to within floating-point precision. Velocities in a .gro file are rotated with the structure but never translated, since a velocity is a direction rather than a position.

Big files stay responsive

Painting a solvated system into the page would mean laying out millions of lines of text, which locks the tab. The preview therefore formats and shows only the first 500 lines, while Download and Copy always produce the complete file. A 200,000-atom system redraws its preview in about 25 ms.

On rotation order. Angles are applied as intrinsic Z‑Y‑X (yaw, then pitch, then roll) matching R = Rz(γ)·Ry(β)·Rx(α). Rotations do not commute, so 90° about X then 90° about Y differs from the reverse order. For a precise orientation, apply one axis at a time.

Frequently asked questions

Which units does each format use?

PDB and XYZ are in ångström; GROMACS .gro is in nanometres (1 nm = 10 Å). When you export to a different format, coordinates are converted automatically, and every input label shows the unit currently in use.

What is the difference between geometric centre and centre of mass?

The geometric centre is the plain arithmetic mean of the coordinates, every atom counts equally. The centre of mass weights each atom by its standard atomic weight, so it sits closer to the heavy atoms. Use centre of mass when setting up a simulation; the two can differ by several ångström in an asymmetric molecule.

Which atomic weights are used?

IUPAC standard atomic weights covering hydrogen through the common heavy elements. If an element cannot be identified from the file the tool falls back to carbon and tells you which symbols were unrecognised, so a mass-weighted result is never silently wrong.

How does the tool know CA is calcium and not an alpha carbon?

It checks the PDB element column first, which is authoritative when present. Failing that it reads the atom name, using the residue name to break ties: CA inside a residue named CA is calcium, while CA in ALA is the alpha carbon.

In what order are rotations applied?

Intrinsic Z-Y-X, yaw about Z, then pitch about Y, then roll about X, equivalent to R = Rz·Ry·Rx acting on a column vector. Because rotations do not commute, apply one axis at a time if you need an exact orientation.

Does rotation or translation distort my molecule?

No. Both are rigid-body operations: every internal distance and angle is preserved exactly. Only the position and orientation of the structure as a whole change.

Can I set my own simulation box?

Yes. The Simulation Box panel lets you type Lx, Ly and Lz in nanometres, or press Fit to Molecule to derive them from the bounding box with a padding percentage. If the source file carried a box (a .gro box line or a PDB CRYST1 record) it is loaded as the starting point. The tool warns you when the box is smaller than the molecule.

Why does the preview stop after 500 lines?

Rendering a large system's full text into the page would freeze the browser. Only the first 500 lines are drawn; Download and Copy always give you the complete file, however large.

Are velocities preserved in GRO files?

Yes. If the input .gro carries velocity columns they are kept, rotated along with the coordinates, and written back out. Velocities are direction vectors, so translating the structure correctly leaves them unchanged.

Can I convert a GRO file to PDB?

Yes. Load the .gro and choose PDB (or XYZ) as the output format; the tool converts nm to Å during export and writes the box as a CRYST1 record.

Is my structure file uploaded anywhere?

No. Files are read and processed entirely in your browser and are never transmitted to a server.

Runs entirely in your browser, no data leaves your device.