On Friday, November 19, 2010 02:55:54 pm Srivastava, Dhiraj (MU-Student) wrote:
> Hi All
> does anyone know any software that can calculate and print out RMSD of
> every residue (c alpha will be good) for homologous structures which has only
> 30-40 % sequence similarity? I looked on the web but all the software that I
> found require the sequence to be the same for both structure.
This is not a well-defined calculation.
In regions where the structures do not superimpose well, how do you
decide which C-alpha pairs with which? What about insertions/deletions?
Usually it only makes sense to calculate RMSD over those residues which
line up structurally, so it won't be "every residue".
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
