[Biojava-dev] [Bug 3138] New: SeqRes2AtomAligner misaligns Atom groups at N-terminus

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3138

           Summary: SeqRes2AtomAligner misaligns Atom groups at N-terminus
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: structure
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: darnells at dnastar.com


The SeqRes2AtomAligner misaligns the N-terminus residues for 1BKV (Collagen)
and 3NLC (VP0956).  Both structures have SEQRES residues without corresponding
ATOM residues at the N-terminus.  In the case of 3NLC, the observed mapping is
(* = no ATOM group):

SEQRES MGHHHHHHSHMIRINE
ATOM   M**********IRINE

and the correct mapping should be:

SEQRES MGHHHHHHSHMIRINE
ATOM   **********MIRINE

Activating the Chemical Component Dictionary does not help the alignment.  Is
it significant that for 1BKV and 3NLC the first SEQRES group and the first ATOM
group are the same residue (nearly the same for 1BKV, PRO ~ HYP)?  Is this a
situation that is difficult for the Needleman-Wunsch algorithm used by
SeqRes2AtomAligner?


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