[Biopython] Error with DSSP module

[João Rodrigues]

Hi Hrishikesh,

In addition to what Carlos suggested, what version of DSSP are you using?
There are a few in circulation nowadays and they're not all consistent in
terms of input arguments and formats.

Cheers,

João

Carlos Henrique <carlosmr12 at gmail.com> escreveu no dia terça, 13/04/2021
à(s) 16:58:

> 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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