Running docker image : BioPython

[pschmidtke]

Hi Harry,

I wanted to run arpeggio using the docker image and the example you provide. I tried:
run --rm -v "$(pwd)":/run -u id -u:id -g -it harryjubb/arpeggio python arpeggio.py /run/1uyk.pdb -s RESNAME:PUX -v

and i get :
INFO//11:52:21.248//Program begin. INFO//11:52:21.321//Loaded PDB structure (BioPython) INFO//11:52:21.701//Loaded PDB structure (OpenBabel) ERROR//11:52:21.712//OpenBabel OBAtom with PDB serial number 1468 could not be matched to a BioPython counterpart. Traceback (most recent call last): File "arpeggio.py", line 759, in <module> raise OBBioMatchError(serial) __main__.OBBioMatchError

Any idea why this happens .... ?

Cheers

Peter

[harryjubb]

Hi Peter,

That's usually an issue with alternate location atoms and/or duplicate atom serial numbers, unfortunately it was difficult to get OpenBabel to distinguish between different alternate locations for the same atom.

I'd recommend choosing choosing / removing alternate locations and seeing if that helps. The webserver does some basic tidying of PDB files to avoid some of the parsing errors.

See also #7, #8, https://github.com/harryjubb/arpeggio#frequently-asked-questions

Thanks for your interest in Arpeggio, let me know if I can help with anything :)

H

[pschmidtke]

ok that makes sense ... I'll try out your cleaning script then. Thanks for the answer. Peter

…

________________________________ From: Harry Jubb <[email protected]> Sent: Friday, April 5, 2019 12:29 To: harryjubb/arpeggio Cc: Peter Schmidtke; Author Subject: Re: [harryjubb/arpeggio] Running docker image : BioPython (#9) Hi Peter, That's usually an issue with alternate location atoms and/or duplicate atom serial numbers, unfortunately it was difficult to get OpenBabel to distinguish between different alternate locations for the same atom. I'd recommend choosing choosing / removing alternate locations and seeing if that helps. The webserver does some basic tidying of PDB files to avoid some of the parsing errors. See also #7<#7>, #8<#8>, https://github.com/harryjubb/arpeggio#frequently-asked-questions Thanks for your interest in Arpeggio, let me know if I can help with anything :) H — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#9 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AOhZZ8kAhn5fcf9p-zIr2K4nrWyc7xKYks5vdyVygaJpZM4ccpmo>.