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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