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Article ID: 451 - Last Modified:

The results of the rmsdcalc script, which I use to perform alignment and rmsd calculations, are not consistent with what I obtain from the Superposition panel in Maestro, and I think that the result from the Maestro tool is more reasonable. Is it possible to use the Maestro superposition facility from the command line?

Unfortunately, the Maestro superposition facility is not available from the command line. There are some ways to obtain better results from the command line, however.

The reason for the discrepancy is that rmsdcalc is mostly used on conformers, so it expects the exact same atom numbering and connectivity. A slight variation (for example 180-degree phenyl ring rotation) can have a dramatic effect on RMSD. There is an automatic renumbering option, -renumber, which investigates alternate atom numbering schemes to identify 180-degree ring twists and other local symmetry operations that may reduce RMSD. You should use caution with this option if your structure has explicit hydrogens since there may be a very large number of ways to renumber hydrogens.

Another option for calculating RMSD is via a Python script,, which is available in the installation. Running it with the following command:

$SCHRODINGER/run  filename1  filename2  -m -a "all"

should also give the same result. The files must be Maestro files. Try the -use_neutral_scaffold option for superimposing all heavy atoms.

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