Skip to content

Coordinate Manipulator

Translate, rotate and re-box a PDB, GRO or XYZ structure, then write it out in any of the three formats with the units converted for you.

Drop a structure file here

or choose one from your computer.

.pdb.ent.gro.xyz

How-to guide

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.

1

Load a structure

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

2

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).

3

Transform

Apply a translation vector, or press Centre on origin to move either the geometric centre or the true centre of mass to (0, 0, 0). For a rotation, type the angles or set the view to Turn molecule and drag it, then press Rotate.

4

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 (O–H 0.957 Å, H–O–H 104.5°) the two are 0.325 Å apart. 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.

Turning it by hand

Set the view to Turn molecule and drag: the molecule turns while the cell and the axes stay where they are, and the three angles follow. The panel shows the rotation matrix, the single turn about one axis it amounts to, and the angle between the molecule’s long axis (or the normal of a flat one) and x, y and z, now and after the turn. Nothing is applied until you press Rotate, and a dragged rotation is kept to a tenth of a degree, so the angles shown are exactly the rotation applied.

Every step, written down

Each rotation, translation and centring is recorded in order. Under the workspace the steps appear as equations, with the matrix or vector each one used and the one transform \mathbf{r}' = M\,\mathbf{r} + \mathbf{d} they add up to, and as a Python script that repeats them: on your file with MDAnalysis, or on any array of coordinates with NumPy alone.

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 the first 5,000 atoms of a larger structure, with Show all to draw the rest, while Download and Copy always produce the complete file. A 200,000-atom system redraws its preview in about 25 ms.

On rotation order. The three angles are applied as a turn about x, then y, then z, each about the fixed axis: R = Rz(γ)·Ry(β)·Rx(α), which is the same as intrinsic Z‑Y‑X and is what gmx editconf -rotate does. Rotations do not commute, so 90° about x then 90° about y differs from the reverse order, and several rotations do not add angle by angle: the editconf command and the equations give the one rotation they add up to.

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. An atom whose element cannot be identified contributes no mass, and the tool names the unrecognised symbols, 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?
A turn about x, then y, then z, each about the fixed axis: R = Rz·Ry·Rx acting on a column vector, which is the same as intrinsic Z-Y-X. Rotations do not commute, so the order matters; the panel shows the matrix and the tilt of the long axis before you apply, and the steps are written out as equations afterwards.
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 5,000 atoms?
Drawing a large system's full text into the page would slow the browser. For a structure of more than 5,000 atoms the preview shows the first 5,000; press Show all to draw the rest. 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.
wwPDB: PDB file format GROMACS: .gro format CIAAW: standard atomic weights Rotation matrices

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