[AMBER] [Bug-Report] NAB: TER record need a serial number

From: Johannes Kalliauer <johannes.kalliauer.tuwien.ac.at>
Date: Mon, 25 Nov 2019 12:06:57 +0100

Dear NAB-Programmers

According to the PDB File Format Specifications (any version) the TER
record need a serial number; for the newest version of the Specifiations
(3.3) see
ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf .
(see page 185)
> The TER record has the same residue name, chain identifier, sequence
> number and insertion code
> as the terminal residue. The serial number of the TER record is one
> number greater than the serial
> number of the ATOM/HETATM preceding the TER.

But however NAB returns TER without serial number (example
from [1]), which is not a problem if you use LeAP, but if you use other
tools it won't be compatible (e.g. see MatLab-Bugrepot below).

I know how to edit it via shell-script, but still that should not be

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:
(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
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
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.

Steve Schäfer
MathWorks Technical Support Department

Self-Service: http://www.mathworks.com/support
File Exchange and MATLAB Answers: http://www.mathworks.com/matlabcentral/

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the appropriate Case.

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Received on Mon Nov 25 2019 - 03:30:02 PST
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