Hi, thanks for the report. I've created an Issue for it on the
internal Amber GitLab server.
On Mon, Nov 25, 2019 at 6:07 AM Johannes Kalliauer
<johannes.kalliauer.tuwien.ac.at> wrote:
> I know how to edit it via shell-script, but still that should not be
> necessary.
Agreed. However, one potential workaround may be to run it through
cpptraj; the cpptraj PDB writer treats TER cards properly:
cpptraj -p old.pdb -y old.pdb -x new.pdb
Hopefully this helps in the short-term.
-Dan
>
> Best Regrads
> Johannes Kalliauer
>
> [1] http://ambermd.org/tutorials/basic/tutorial1/section2.htm
>
> -------- Weitergeleitete Nachricht --------
> Betreff: Re: pdbread does not recognise TER correclty [
> ref:_00Di0Ha1u._5000Z151OgB:ref ]
> Datum: Tue, 25 Sep 2018 08:54:17 +0000 (GMT)
> Von: Steve Schäfer <support.mathworks.de>
> An: e1027477.student.tuwien.ac.at <e1027477.student.tuwien.ac.at>
>
>
>
> Dear Johannes Kalliauer,
>
> the reason for the observed behavior is as follows:
> A lthough AMBER and Chimera may support TER records with no atom number,
> this is not compliant with the PDB file specification
> that pdbread & pdbwrite are based on:
> https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/format2.3-0108-us.pdf.
> (see page 165).
> Due to the length and complexity of the PDB spec, it is unlikely that we
> will be able to support non-standard behavior to match other third-party
> software.
> Sorry that we cannot relief you from the amount of manual work in your
> workflow. You might be able to automate parts of it using regexp
> <https://blogs.mathworks.com/loren/2012/10/18/learning-to-love-regular-expressions/>
> or other tools.
>
> Kind regards,
> Steve Schäfer
>
>
> --------------- Original Message ---------------
> *From:* DE MathWorks Support [support.mathworks.de]
> *Sent:* 24.09.2018 17:38
> *To:* e1027477.student.tuwien.ac.at
> *Subject:* Re: pdbread does not recognise TER correclty [ ]
>
> Dear Johannes Kalliauer,
>
> I am writing in reference to your Technical Support Case 03251158
> regarding 'pdbread does not recognise TER correclty'.
> Thank you very much for sharing reproduction code and data with us. I
> will look into the problem and try to provide you with a feasible
> workaround for this issue.
> Pointing us to this short coming of a particular functionality is very
> helpful and highly appreciated.
>
> Sincerely,
> Steve Schäfer
> MathWorks Technical Support Department
>
> Self-Service: http://www.mathworks.com/support
> File Exchange and MATLAB Answers: http://www.mathworks.com/matlabcentral/
>
> Please preserve the Reference ID in further correspondence on this
> query. This allows our systems to automatically associate your reply to
> the appropriate Case.
>
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> Barbo, Jeanne O’Keefe
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>
> ref:_00Di0Ha1u._5000Z151OgB:ref
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Received on Mon Nov 25 2019 - 05:30:03 PST
