[Biopython] Error with DSSP module

[Carlos Henrique]

Hi Hrishikesh,

Can you provide more details on the PDB structure you are using as input?
I had similar problems in the past and in my case it was because DSSP was
failing due to issues with the protein structure. In order to rule that
out, you could try running DSSP manually in a terminal window and check the
output/log file.
Something like this:

*dssp -i 1crn.pdb -o 1crn.dssp*

I hope this helps.

Cheers,

On Tue, 13 Apr 2021 at 23:51, Hrishikesh Dhondge <hbdhondge at gmail.com>
wrote:

> Hello everyone,
> I'm facing a problem with the DSSP module in Biopython. I am trying to
> compute solvent accessible surface area from the PDB file.
> I used the same block of code as given in the biopython wiki:
>
>
> https://biopython.org/docs/1.78/api/Bio.PDB.DSSP.html?highlight=dssp#module-Bio.PDB.DSSP
>
> But after running it returns nothing and gives the following error:
>
> a_key = list(dssp.keys())[2]
> IndexError: list index out of range
>
> Any suggestions would be appreciated. Thanks in advance!
>
> --
> With regards
> Hrishikesh Dhondge
>
> _______________________________________________
> Biopython mailing list  -  Biopython at biopython.org
> https://mailman.open-bio.org/mailman/listinfo/biopython
>


-- 
Carlos Rodrigues
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