[Biojava-l] Chain order

[Jose Duarte]

I'm not fully understanding the issue. Can you explain how your calculation
is affected by the order? What are you trying to calculate? Please note
that you can decide the order you need in your implementation.

One thing that you can do is use polymeric chains only
(structure.getPolymerChains()), for instance that will not include the CU
HETATM in your example. That may or may not be what you want, but I can't
tell without more details.

Also as a general recommendation to anyone dealing with PDB data: please
note that the PDB format is the legacy format and it is not recommended to
use it anymore. The main format for PDB data is PDBx/mmCIF. In fact an
increasingly higher number of PDB entries in the archive are not available
in PDB format anymore. That will grow even more next year once 5-letter
chemical component identifiers start to be used.

Hope this helps

Jose
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