RMSD in R: HELP

Question

[fyfes]

Hi, I have to calculate RMSD between two proteins in Rstudio from PDB but I am not sure if I am doing it right. Could you please take a look at my code and tell me if I do it right?

Thanks

library( "bio3d" )

a_pdb = read.pdb('1bg2')
b_pdb = read.pdb('1i6i')
pdbs <- list(a_pdb, b_pdb)

aln_pdbs <- pdbaln(pdbs)

inds <- gap.inspect(aln_pdbs$xyz)

rmsd(a=a_pdb$xyz, b=b_pdb$xyz, a.inds=inds$f.inds, b.inds=inds$f.inds, fit=TRUE)

[Ram]

Do you have any evidence that you're either doing it right or wrong? If not, you're just asking you to verify your code for you.

[fyfes]

well yes I have a hint that I am doing sth wrong as I am using PDBeFOLD and I have different results than from R studio

[Ram]

Are the RMSD calculation algorithms the same between PDBeFOLD and your code above?

[fyfes]

i am not sure as I am unable to find documentation on R algoritm. I just would like to know if my R script is correct

[Ram]

The paper mentioned here should detail how the rmsd function calculates RMSD.

EDIT: It should, but it doesn't. Looks like reading their code is the only way to get details on their algorithm, and that's not optimal. I hope someone here has experience with this stuff and can help you see what differences might exist.