How to associate secondary structure to protein sequence

Question

[francesco.costa.11]

Hi everybody! I am sruggling to find a way to associate to a vast collection of PDB entries the respective secondary structures. For every protein sequence It would be nice to have every aminoacid associated to the secondary structure, like in the image:

I am not looking for secondary structure predictions but for the secondary structure data stored in the PDF files. Does anyone know a program or a Python/R script to rapidly do that on a large amount of PDBs?

Answer 1

[fracarb8]

[dssp][1] does exactly that.

You can run it on it's own, or you can use it as plugin. For example, pyMol support it, and you can process al pdb you need with a python script.

[francesco.costa.11]

Thank you!