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
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