Calculate the RMSD and maximum atomic displacement between a reference structure and a set of conformers. The set of atoms to superpose can be defined via an ASL expression. The following ASL expression has a special meaning:

  • all = all atoms in the reference and comparison structures
Note that the number of atoms used in the comparison has to be identical. This is usually not a problem with conformers of course but can be problematic when comparing different molecules and using the ASL expression 'all'.

Backend implementation

$SCHRODINGER/run rmsd.py


Column containing input 1
Column in the first input data table containing the reference structure.
Column containing input 2
Column in the second input data table containing the comparison molecules.
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

ASL Expression
Set of atoms to superimpose. It also accepts a SMARTS using the following syntax: SMARTS. 'c1ccccc1'
Skip atom number scheme normalization
Skip atom number scheme normalization for faster calculation. However, this flag will cause the script to generate inaccurate results if the input structures have different atom numbering schemes.
Ignore ionization and tautomer states
Ignore ionization and tautomer states by reducing the structures to a skeleton of neutral heavy atoms connected with single bonds. This facilitates the comparison of structures that are not true conformers, but are closely related.
Evaluate just the substructures created using the ASL expression
Evaluate just the substructures created by extracting the atoms that form the ASL expression. This speeds up calculations involving large structures, when only a small portion is needed for the RMSD. e.g. reference is a ligand and comparison table contains receptor-ligand complexes. This option is also useful for comparing a shared substructure found in non-conformers. e.g. create substructure conformers from non-conformers on the fly.
Compute Matrix
Whether the distance matrix should be calculated (on by default)
Type of RMS alignment
Transform test structure(s) as a rigid body onto the reference, then calculate RMS alignment.

Input Ports

Reference Molecule in Maestro format
Comparison Molecules in Maestro format

Output Ports

Superposed Molecules in Maestro format
Matrix is calculated for all members of first input against all members of second input


Log output of RMSD
Log output of RMSD




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