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Article ID: 448 - Last Modified: December 4, 2010

I would like to run a superposition from the command line and not from the graphical interface. Is there any way to script such an operation?

You can try one of the Python scripts available from our Script Center under "Command Line RMSD Calculation". Once installed, run the following command to get the usage statement:

$SCHRODINGER/run rmsd.py -h

You should be able to use -asl option to define the ASL string in the same way as it is done in Maestro.

Please note that superposition generally requires ligands to be conformers, with identical atom numbering and connectivity. If you get inconsistent results, you can try running the rmsd.py script with the "-use_neutral_scaffold" option.

Keywords: superimpose , script, command line, rmsd.py

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