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Re: [modeller_usage] Per-residue RMSD

On 4/13/22 11:00 PM, Karolina Mitusińska (Markowska) wrote:
I would like to compare my predicted model with a crystal structure. I know how to calculate RMSD between these two models, but I would also like to have more detailed information on the RMSD between corresponding atoms, for example C-alphas.

Perhaps I am misunderstanding what you want to do here, but the RMSD between a single pair of atoms is just the Cartesian distance. So you can call superpose() to first fit the two models:

Then access the two Atom objects you're interested in and calculate the distance in Python using their x,y,z coordinates:

If you mean you want the RMSD over *all* C-alphas or some other subset, first do superpose() to fit the models, then select that subset of atoms and do superpose() again with fit=False. This won't change the superposition but will report the RMSD of the subset.

	Ben Webb, Modeller Caretaker
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage