Re: [modeller_usage] Per-residue RMSD

[Modeller Caretaker <>]

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
--
             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage