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/
