[Biopython] Using DSSP to calculate SASA

[Ahmad Abdelzaher]

Thank you. This script is most helpful. I still want to know how to
change the default values from sander to miller? Can I use external
reference values from a recent paper?

P.s. obviously I can go to the DSSP class and override sander values
with whatever values I want, but I was hoping for a way to do it via
the class argument or something, if there's one.

Regards.

On Tue, Apr 25, 2017 at 12:36 AM, João Rodrigues
<j.p.g.l.m.rodrigues at gmail.com> wrote:
> I don't know what you are doing with Pymol so I cannot compare.
>
> To access from the DSSP data you have two options. First, access it directly
> using the dictionary-like structure it returns, which is what you are trying
> to do. The simpler way is to access the xtra method of each residue in your
> structure. See this example:
> https://gist.github.com/JoaoRodrigues/fd66a4ded49974b19730758a6f8f8e51
>
> The EXP_DSSP_RASA is the R(elative)ASA, which is the absolute value from
> DSSP normalized by the scales you can find in the Python file. We should
> work on the documentation indeed if it is so confusing.
>
> Freesasa is not in Biopython but it does have a Python API.