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harryjubb / arpeggio

Calculation of interatomic interactions in molecular structures
http://biosig.unimelb.edu.au/arpeggioweb/
GNU General Public License v3.0
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Running docker image : BioPython #9

Closed pschmidtke closed 5 years ago

pschmidtke commented 5 years ago

Hi Harry,

I wanted to run arpeggio using the docker image and the example you provide. I tried:
run --rm -v "$(pwd)":/run -uid -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 commented 5 years ago

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 https://github.com/harryjubb/arpeggio/issues/7, https://github.com/harryjubb/arpeggio/issues/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 commented 5 years ago

ok that makes sense ... I'll try out your cleaning script then.

Thanks for the answer.

Peter

From: Harry Jubb notifications@github.com 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 #7https://github.com/harryjubb/arpeggio/issues/7, #8https://github.com/harryjubb/arpeggio/issues/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

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