Re: Chain order
Enrico Morelli <[email protected]> Fri, 13 Oct 2023 10:16:14 +0200
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
--===============4556616030341493593== Content-Type: multipart/alternative; boundary=----Y6QZX4IQ3ZYUDREY8RD0WUW947T6K6 Content-Transfer-Encoding: 7bit ------Y6QZX4IQ3ZYUDREY8RD0WUW947T6K6 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable I read a pdb or download it using BioJava=2E 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) =2E For = my calculation I read the pdb I created and I'm aspecting that the first li= ne 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= =2E I hope you understand well my problem=2E I need to read the new pdb in seq= uential order and maintain the sequential order also in the getChain loop= =2E Il 13 ottobre 2023 05:48:40 CEST, Jose Duarte <jose=2Eduarte@rcsb=2Eorg> h= a scritto: >I'm not fully understanding the issue=2E Can you explain how your calcula= tion >is affected by the order? What are you trying to calculate? Please note >that you can decide the order you need in your implementation=2E > >One thing that you can do is use polymeric chains only >(structure=2EgetPolymerChains()), for instance that will not include the = CU >HETATM in your example=2E That may or may not be what you want, but I can= 't >tell without more details=2E > >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 t= o >use it anymore=2E The main format for PDB data is PDBx/mmCIF=2E In fact a= n >increasingly higher number of PDB entries in the archive are not availabl= e >in PDB format anymore=2E That will grow even more next year once 5-letter >chemical component identifiers start to be used=2E > >Hope this helps > >Jose ----------------------------------------------------------- =C2=A0 Enrico Morelli =C2=A0 System Administrator | Programmer | Web Developer =C2=A0 CERM - Polo Scientifico =C2=A0 via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY =C2=A0----------------------------------------------------------- ------Y6QZX4IQ3ZYUDREY8RD0WUW947T6K6 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable <html><head></head><body><div dir=3D"auto">I read a pdb or download it usin= g BioJava=2E=C2=A0 After that I extract a metal and some ligands from the p= db and I create a new pdb file with the metal as first line followed by its= ligands (has you saw in the last mail) =2E For my calculation I read the p= db I created and I'm aspecting that the first line is the metal, but BioJav= a order the pdb chains in alphabetical order so I haven't the metal in the = aspected position and my calculation goes wrong=2E<br><br>I hope you unders= tand well my problem=2E I need to read the new pdb in sequential order and = maintain the sequential order also in the getChain loop=2E</div><br><br><di= v class=3D"gmail_quote"><div dir=3D"auto">Il 13 ottobre 2023 05:48:40 CEST,= Jose Duarte <jose=2Eduarte@rcsb=2Eorg> ha scritto:</div><blockquote = class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0=2E8ex; border-left: 1p= x solid rgb(204, 204, 204); padding-left: 1ex;"> <div dir=3D"ltr">I'm not fully understanding the issue=2E Can you explain = how your calculation is affected by the order? What are you trying to calcu= late? Please note that you can decide the order you need in your implementa= tion=2E <div><br></div><div>One thing that you can do is use polymeric= chains only (structure=2EgetPolymerChains()), for instance that will not i= nclude the CU HETATM in your example=2E That may or may not be what you wan= t, but I can't tell without more details=2E</div><div><br></div><div>Also a= s a general recommendation to anyone dealing with PDB data: please note tha= t the PDB format is the legacy format and it is not recommended to use it a= nymore=2E The main format for PDB data is PDBx/mmCIF=2E In fact an increasi= ngly higher number of PDB entries in the archive are not available in PDB f= ormat anymore=2E That will grow even more next year once 5-letter chemical = component identifiers start to be used=2E </div><div><br></div><div>Ho= pe this helps</div><div><br></div><div>Jose</div><div><br></div></div> </blockquote></div><div dir=3D"auto"><hr>=C2=A0 Enrico Morelli<br>=C2=A0 S= ystem Administrator | Programmer | Web Developer<br><br><br>=C2=A0 CERM - P= olo Scientifico<br>=C2=A0 via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - IT= ALY<hr></div></body></html> ------Y6QZX4IQ3ZYUDREY8RD0WUW947T6K6-- --===============4556616030341493593== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Biojava-l mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biojava-l --===============4556616030341493593==--