RMSD of two homologues proteins

Question

[Mike]

Hi,

I'm looking for the easiest way of calculating RMSD between two homologous proteins. (i.e. sequences do not match perfectly). Until now I was using Chimera software, where steps are as follow:

1. Calculating pairwise alignment
2. Then structures are superimposed
3. RMSD is calculated between corresponding amino acids in alignment.

And this work quite well, but I'm looking for something simpler that I can use in python script. Preferably in with no need of running subprocess.

Answer 1

[a.polo88]

you can create a script for pymol that function with python script or directly from the software can be possible. otherwise there are many of packages in R for example BIO3D can be useful.

https://pypi.python.org/pypi/pyRMSD/4.0.0 can be useful.