<html><head></head><body><div dir="auto">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.<br><br>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.</div><br><br><div class="gmail_quote"><div dir="auto">Il 13 ottobre 2023 05:48:40 CEST, Jose Duarte <jose.duarte@rcsb.org> ha scritto:</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div dir="ltr">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. <div><br></div><div>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.</div><div><br></div><div>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. </div><div><br></div><div>Hope this helps</div><div><br></div><div>Jose</div><div><br></div></div>
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