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
http://ambermd.org/tutorials/basic/tutorial1/files/pdb_files/nuc.pdb
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
necessary.
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.
The MathWorks GmbH | Friedlandstr.18 | 52064 Aachen | District Court
Aachen | HRB 8082 | Managing Director: Andreas Schindler, Steven D.
Barbo, Jeanne O’Keefe
ref:_00Di0Ha1u._5000Z151OgB:ref
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 25 2019 - 03:30:02 PST
