First off, many thanks to those who responded on- and off-BB. This kind of approach seems to be the best way forward. I’ll probably avoid using “~" in the names, because I suspect that many older programs will barf on them, but using HETNAM & HET should make my life relatively easy (and is documented at https://www.wwpdb.org/documentation/file-format).
Since I’m not working from mmCIF files I won’t use Gemmi (or is that “gemmi”?) but this does give me what should be a robust way forward. best wishes Harry > On 20 Nov 2025, at 14:51, Marcin Wojdyr > <[email protected]> wrote: > > Thanks Paul, > > BTW, I call it the tilde-hetnam extension of the PDB format: > https://gemmi.readthedocs.io/en/stable/mol.html#tilde-hetnam > "The tilde-hetnam extension addresses this issue: a long CCD code is > substituted with a 3-character alias that starts with a tilde (~); the > original code is stored in columns 72-79 of the HETNAM record." > But I don't think any other project decided to implement it. Although > programs that use gemmi library will handle such PDB files > automatically, though. > > Marcin > > On Thu, Nov 20, 2025 at 3:26 PM Paul Bond > <[email protected]> wrote: >> >> 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 > > ######################################################################## > > 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/
