I'm starting from crystallographic coordinates for a ligand from a protein/ligand complex. I would like to compare the RMSD of the generated conformers to the crystallographic coordinates. How do I do that?

You can use Tools → Superposition in Maestro. If you make sure that all the conformers are selected (highlighted) in the Project Table and that the input structure to the search is above the output conformers in the table, you can select 'Create property' in the Superposition panel and the RMSD values will be added to the Project Table for the selected entries when you do the superposition. You can superimpose based on all atoms, all heavy atoms, or any other subset of the ligand atoms.

We also have a script on our Script Center called rmsd.py that will perform the RMSD calculations for you from the command line.

Keywords: conformational search, RMSD, Maestro

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