A chromophore is the part of a molecule responsible for its color. Several proteins, such as GFP contain a chromopohre that consists of three modified residues. BioJava represents this as a single group in terms of atoms, however as three amino acids when creating the amino acid sequences.

// make sure we download chemical component definitions

// which is required for correctly representing the chromophore

FileParsingParameters params = new FileParsingParameters();

params.setLoadChemCompInfo(true);

// now register the parameters in the cache

AtomCache cache = new AtomCache();

cache.setFileParsingParams(params);

StructureIO.setAtomCache(cache);

// request a GFP protein

Structure s1 = StructureIO.getStructure("2pxw");

// and print out the internals

System.out.println(s1.getPDBHeader().toPDB());

for ( Chain c : s1.getChains()) {

System.out.println("Chain " + c.getChainID() +

" internal " + c.getInternalChainID() +

" ligands " + c.getAtomLigands().size());

System.out.println(" 10 20 30 40 50 60");

System.out.println("1234567890123456789012345678901234567890123456789012345678901234567890");

System.out.println(c.getAtomSequence());

int pos = 0 ;

for (Group g: c.getAtomGroups()) {

pos++;

System.out.println(pos + " " + g.getResidueNumber() + " " + g.getPDBName() + " " + g.getType() + " " + g.getChemComp().getOne_letter_code() + " " + g.getChemComp().getType() );

}

}