[Biojava-l] Chain order

[Enrico Morelli]

I read a pdb or download it using BioJava.  After that I extract a metal and some ligands from the pdb and I create a new pdb file with the metal as first line followed by its ligands (has you saw in the last mail) . For my calculation I read the pdb I created and I'm aspecting that the first line is the metal, but BioJava order the pdb chains in alphabetical order so I haven't the metal in the aspected position and my calculation goes wrong.

I hope you understand well my problem. I need to read the new pdb in sequential order and maintain the sequential order also in the getChain loop.

Il 13 ottobre 2023 05:48:40 CEST, Jose Duarte <jose.duarte at rcsb.org> ha scritto:
>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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  Enrico Morelli
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