Re: [modeller_usage] Denovo loop remodeling

On 06/28/2013 08:43 AM, Ramin Ekhteiari wrote: > Is there any rmsd-energy.py script in modeller to calculate the RMSD and > energy of all generated pdb files with template.

You can use selection.superpose() to get the RMSD, but RMSD between target and template is essentially meaningless (a better comparison for benchmarking would be against the native structure of the target sequence). loopmodel already gives you the energies (they're also in the generated PDB files).

Ben Webb, Modeller Caretaker