Calculate molecule RMSD
Compare two molecules by root-mean-square deviation after optimal alignment. Choose the input format and alignment methods, then calculate in the browser.
Molecule pair
Provide two molecules in the selected format. Upload files or paste structure data for each molecule.
or drop a file here
or drop a file here
RMSD result
RMSD value will appear here after calculation.
Calculate molecule RMSD matrix
Compute pairwise RMSD values for a set of structures in one job. Upload at least two molecule files to populate the matrix.
0 molecules
Estimated cost: $— (~—)
Molecule files
Upload a directory, multiple structure files, or a ZIP archive. All structure files must use the same supported extension (`.mol`, `.mol2`, `.pdb`, or `.xyz`). ZIP archives may contain nested folders.
No molecule files uploaded yet.
or drop structure files here
Alignment options
Choose structure format and alignment settings applied to every pairwise comparison in the matrix.