[Biopython-dev] [Bug 2292] New: Bio.PDBIO writes TER records without any required fields

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2292

           Summary: Bio.PDBIO writes TER records without any required fields
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Other
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: misiek at genesilico.pl


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.


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