Hi Harry, If you need to produce PDB files from CIF files with 5-letter ligand codes you can use gemmi convert, e.g.:
gemmi convert gemmi convert 8XFM.cif 8XFM.pdb --shorten-tlc The original has a ligand called A1LU6. In the PDB file it gets a HET and HETNAM entry: HET ~U6 A 401 25 real CCD code: A1LU6 HET EDO A 402 4 HET ZN A 403 1 HETNAM ~U6 A1LU6 Then in the atom lines it is referred to by the new ID: HETATM 2209 CL ~U6 A 401 38.210 38.396 16.715 1.00 77.22 CL HETATM 2210 C17 ~U6 A 401 38.401 39.551 15.377 1.00 54.65 C HETATM 2211 C16 ~U6 A 401 37.332 40.370 15.083 1.00 52.11 C HETATM 2212 C15 ~U6 A 401 37.438 41.271 14.038 1.00 51.08 C HETATM 2213 C14 ~U6 A 401 38.616 41.345 13.308 1.00 48.95 C If you convert it back to CIF with gemmi: gemmi convert 8XFM.pdb new.cif Then the resulting mmCIF file just uses the original A1LU6 naming. Cheers, Paul On Thu, 20 Nov 2025 at 12:54, Harry Powell < [email protected]> wrote: > Hi folks > > The real answer (before I ask the question) is, of course, to use mmCIF. > But quite a few programs out there don’t read mmCIF files properly (if at > all), so I’ll ask the question anyway. > > The venerable PDB format allows 3 columns (18-20) for the residue or > ligand name, and this was fine as long as there were only chemical > components allowed with 3 characters - but now there are loads that have 5 > characters (e.g. A1B20 - see > https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/A1B20). > > If I wanted to write a PDB format file for the ligand that had the > 5-character code, what would be the “best” way to do it (of course, there > are different definitions of “best”…)? > > What dirty trick would cause the least damage (at least, to common > programs)? > > Allowing the ligand name to spread over columns 16-20 *might* work, but > that would mean encroaching on the atom name column, and might cause > confusion between things like calcium (“CA “) and carbons labelled with an > “A” (“ CA”). > > 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/
