Re: [Biopython] Error with DSSP module

According to the Biopython issue I linked to, DSSP v4.0 is not going
to work (until someone helps update Biopython).

Peter

On Tue, Apr 13, 2021 at 3:25 PM Hrishikesh Dhondge <[email protected]> wrote:
>
> Hello,
>
> I'm using Biopython version 1.78. And when I checked for the DSSP version using 'mkdssp --version'; it showed me 'mkdssp version 62 2021-04-13'.
>
> I installed DSSP from the following git repo: https://github.com/PDB-REDO/dssp
>
> Please let me know if I did something wrong here.
>
> On Tue, Apr 13, 2021 at 3:57 PM Peter Cock <[email protected]> wrote:
>>
>> Which version of DSSP are you using? See:
>>
>> https://github.com/biopython/biopython/issues/3433
>>
>> Peter
>>
>> On Tue, Apr 13, 2021 at 2:51 PM Hrishikesh Dhondge <[email protected]> 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  -  [email protected]
>> > https://mailman.open-bio.org/mailman/listinfo/biopython
>
>
>
> --
> With regards
> Hrishikesh Dhondge
> PhD student,
> LORIA - INRIA Nancy
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