[Biojava-l] exception in DisplayAFP.createArtificialStructure

[Daniel Asarnow]

Hello again,
I'm getting a null value from DisplayAFP.createArtificialStructure after a
successful alignment.  It appears that the Groups in hetatms aren't set or
are missing their Atom; There is a StructureException ("no atom found at
position 0") thrown from the Group.getAtom call at DisplayAFP line 487
(inside the getAtomArray call at line 679).

Here is my code:

Structure structure1 = cache.getStructure("2hhb.A"); // Hb A chain
Structure structure2 = cache.getStructure("2v1k.A"); // Mb
Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
Atom[] ca2 = StructureTools.getAtomCAArray(structure2);
StructureAlignment alignment =
StructureAlignmentFactory.getAlgorithm(algorithmName);
AFPChain afpChain = alignment.align(ca1, ca2, params); // successful w/
correct alignment score
artificial = DisplayAFP.createArtificalStructure(afpChain, ca1, ca2); //
returns null

This is with the 3.0.2 snapshot JARs.
I'm a missing something or is this a bug?

Thanks!

-da