Hi Rafael That would be okay for current PDB entries - I don’t actually know of any for which the IDs break out into the pdb_0000 prefix yet.
However, I can’t borrow other PDB ids because sometimes I would need to be able to reference the correct entry from my re-written PDB. Best wishes Harry > On 15 Jul 2026, at 15:20, Rafael Marques <[email protected]> wrote: > > Hi Harry, > > If the file format is the problem, what I tend to do, for practical terms, is > opening the .mmCIF file in Pymol and save it as .pdb. I have never faced > myself a problem because the name of the file is not XXXX.pdb or it is > blablablabla.pdb as long the extension is still .pdb. If, for whatever > reason, a software needs a four letter code to work, I would just borrow an > existing pdb code and change it later on (like if you are about to deposit) > to its appropriate name. > > Best wishes > > ______________________________________________________ > > Rafael Marques da Silva > PhD Student – Structural Biology > University of Leicester > > Mestre em Física Biomolecular > Universidade de São Paulo > > Bacharel em Ciências Biológicas > Universidade Federal de São Carlos > > phone: +44 07861 273773 > > "A sorte acompanha uma mente bem treinada" > ________________________________________________ > De: CCP4 bulletin board <[email protected]> em nome de Harry Powell > <[email protected]> > Enviado: quarta-feira, 15 de julho de 2026 12:42 > Para: [email protected] <[email protected]> > Assunto: [ccp4bb] "Correct" way to deal with longer PDB entry IDs in PDB > format files? > > Hi folks > > Probably a naïve question, but although I try to work with mmCIF files, > occasionally I need to convert coordinates to the legacy PDB format for > legacy programs that simply don’t understand mmCIF and never will. > > One thing that I need to do is to write the PDB ID into the HEADER line in > the PDB file; conventionally, I’d write this into columns 63-66 (as per the > documentation), and this is fine while I have an entry like “pdb_00007al9”; > however, what should I do if I have an entry like “pdb_00237al9”? > > I can see that this will probably never have a single correct answer since we > should all be using mmCIF anyway, but I wondered what other people might do? > > I’d be inclined to extend the ID into columns 60 - 63, which would future > proof _me_ until I retire properly, but might not work for the young folk who > will be working long after that! > > Thoughts? > > Harry > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
