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: https://salilab.org/modeller/10.2/manual/node255.html
Then access the two Atom objects you're interested in and calculate the distance in Python using their x,y,z coordinates: https://salilab.org/modeller/10.2/manual/node383.html
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