[Biopython-dev] [Biopython (old issues only) - Bug #2292] (Closed) Bio.PDBIO writes TER records without any required fields

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Fri Mar 24 10:40:30 UTC 2017

Issue #2292 has been updated by Peter Cock.

Status changed from Resolved to Closed

Pull request merged with fix from Michal.

Bug #2292: Bio.PDBIO writes TER records without any required fields

* Author: Michal J.
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Other
* Target version: Not Applicable
* URL: 
Bio.PDBIO is happy to write TER records as "TER\n", which is inconsistent with PDB format specification.

The PDB format requires that TER records have some fields similar to ATOM records:
'''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.'''

[See http://www.wwpdb.org/documentation/format23/sect9.html#TER]

It leads to problem with programs that require correct TER records (like multiple structural alignment program MUSTANG), and crash when they are not found.

PDBIO.diff (656 Bytes)

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